@jbrowse/core 2.0.1 → 2.1.0
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/BaseFeatureWidget/BaseFeatureDetail.d.ts +6 -0
- package/BaseFeatureWidget/BaseFeatureDetail.js +313 -592
- package/BaseFeatureWidget/SequenceFeatureDetails.js +213 -479
- package/BaseFeatureWidget/index.js +88 -126
- package/BaseFeatureWidget/types.js +1 -4
- package/BaseFeatureWidget/util.js +40 -75
- package/CorePlugin.js +55 -94
- package/Plugin.js +9 -34
- package/PluginLoader.js +153 -422
- package/PluginManager.d.ts +17 -14
- package/PluginManager.js +377 -666
- package/ReExports/Attributes.js +3 -10
- package/ReExports/BaseCard.js +3 -10
- package/ReExports/DataGrid.js +5 -12
- package/ReExports/FeatureDetails.js +3 -10
- package/ReExports/index.js +6 -12
- package/ReExports/list.d.ts +5 -0
- package/ReExports/list.js +271 -7
- package/ReExports/material-ui-colors.js +15 -16
- package/ReExports/modules.d.ts +0 -1
- package/ReExports/modules.js +453 -798
- package/TextSearch/BaseResults.js +51 -123
- package/TextSearch/TextSearchManager.js +66 -144
- package/assemblyManager/assembly.js +280 -555
- package/assemblyManager/assemblyConfigSchema.js +47 -64
- package/assemblyManager/assemblyManager.js +126 -272
- package/assemblyManager/index.js +9 -22
- package/configuration/configurationSchema.js +167 -203
- package/configuration/configurationSlot.js +248 -326
- package/configuration/index.js +19 -35
- package/configuration/util.js +131 -173
- package/data_adapters/BaseAdapter.d.ts +2 -2
- package/data_adapters/BaseAdapter.js +132 -521
- package/data_adapters/CytobandAdapter.js +40 -126
- package/data_adapters/dataAdapterCache.js +77 -158
- package/package.json +4 -5
- package/pluggableElementTypes/AdapterType.js +24 -79
- package/pluggableElementTypes/AddTrackWorkflowType.d.ts +17 -0
- package/pluggableElementTypes/AddTrackWorkflowType.js +20 -0
- package/pluggableElementTypes/ConnectionType.js +22 -65
- package/pluggableElementTypes/DisplayType.js +35 -82
- package/pluggableElementTypes/InternetAccountType.js +23 -64
- package/pluggableElementTypes/PluggableElementBase.js +8 -20
- package/pluggableElementTypes/RpcMethodType.js +85 -427
- package/pluggableElementTypes/TextSearchAdapterType.js +16 -55
- package/pluggableElementTypes/TrackType.js +26 -70
- package/pluggableElementTypes/ViewType.js +21 -63
- package/pluggableElementTypes/WidgetType.js +21 -64
- package/pluggableElementTypes/index.d.ts +4 -3
- package/pluggableElementTypes/index.js +42 -125
- package/pluggableElementTypes/models/BaseConnectionModelFactory.js +28 -43
- package/pluggableElementTypes/models/BaseDisplayModel.js +58 -95
- package/pluggableElementTypes/models/BaseTrackModel.js +139 -199
- package/pluggableElementTypes/models/BaseViewModel.js +24 -40
- package/pluggableElementTypes/models/InternetAccountModel.js +116 -263
- package/pluggableElementTypes/models/baseConnectionConfig.js +14 -25
- package/pluggableElementTypes/models/baseInternetAccountConfig.js +29 -38
- package/pluggableElementTypes/models/baseTrackConfig.js +106 -133
- package/pluggableElementTypes/models/index.js +21 -70
- package/pluggableElementTypes/renderers/BoxRendererType.js +132 -291
- package/pluggableElementTypes/renderers/CircularChordRendererType.js +8 -38
- package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +60 -192
- package/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -2
- package/pluggableElementTypes/renderers/FeatureRendererType.js +89 -264
- package/pluggableElementTypes/renderers/RendererType.js +31 -105
- package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +61 -72
- package/pluggableElementTypes/renderers/ServerSideRendererType.js +112 -265
- package/pluggableElementTypes/renderers/index.js +19 -62
- package/pluggableElementTypes/renderers/util/serializableFilterChain.js +27 -65
- package/rpc/BaseRpcDriver.js +169 -405
- package/rpc/MainThreadRpcDriver.js +27 -150
- package/rpc/RpcManager.js +58 -159
- package/rpc/WebWorkerRpcDriver.js +54 -171
- package/rpc/configSchema.js +25 -49
- package/rpc/coreRpcMethods.js +221 -959
- package/rpc/remoteAbortSignals.js +46 -70
- package/tsconfig.build.tsbuildinfo +1 -1
- package/ui/AboutDialog.js +106 -162
- package/ui/App.js +157 -242
- package/ui/AssemblySelector.js +59 -120
- package/ui/CascadingMenu.js +101 -196
- package/ui/ColorPicker.d.ts +16 -0
- package/ui/ColorPicker.js +97 -0
- package/ui/Drawer.js +28 -61
- package/ui/DrawerWidget.js +108 -202
- package/ui/DropDownMenu.js +60 -91
- package/ui/EditableTypography.js +87 -149
- package/ui/ErrorMessage.js +41 -56
- package/ui/FactoryResetDialog.js +24 -57
- package/ui/FatalErrorDialog.js +59 -91
- package/ui/FileSelector/FileSelector.js +123 -189
- package/ui/FileSelector/LocalFileChooser.js +44 -75
- package/ui/FileSelector/UrlChooser.js +17 -38
- package/ui/FileSelector/index.js +6 -12
- package/ui/Icons.js +45 -69
- package/ui/Logo.js +57 -110
- package/ui/Menu.js +232 -354
- package/ui/PrerenderedCanvas.js +63 -87
- package/ui/ResizeHandle.js +87 -116
- package/ui/ReturnToImportFormDialog.js +32 -63
- package/ui/SanitizedHTML.js +64 -47
- package/ui/Snackbar.js +74 -101
- package/ui/SnackbarModel.js +37 -51
- package/ui/Tooltip.js +49 -76
- package/ui/ViewContainer.js +113 -196
- package/ui/colors.d.ts +10 -0
- package/ui/colors.js +78 -0
- package/ui/index.js +51 -181
- package/ui/react-colorful.d.ts +17 -0
- package/ui/react-colorful.js +455 -0
- package/ui/theme.js +199 -247
- package/util/Base1DUtils.js +163 -202
- package/util/Base1DViewModel.js +121 -168
- package/util/QuickLRU.js +84 -332
- package/util/TimeTraveller.d.ts +19 -0
- package/util/TimeTraveller.js +86 -0
- package/util/aborting.js +49 -127
- package/util/analytics.js +91 -154
- package/util/blockTypes.js +106 -240
- package/util/calculateDynamicBlocks.js +98 -128
- package/util/calculateStaticBlocks.js +105 -125
- package/util/color/cssColorsLevel4.js +156 -160
- package/util/color/index.js +33 -55
- package/util/compositeMap.js +49 -333
- package/util/formatFastaStrings.js +9 -14
- package/util/idMaker.js +18 -31
- package/util/index.d.ts +7 -20
- package/util/index.js +742 -1188
- package/util/io/RemoteFileWithRangeCache.js +88 -257
- package/util/io/index.js +95 -169
- package/util/jexl.js +60 -115
- package/util/jexlStrings.js +24 -29
- package/util/layouts/BaseLayout.js +1 -4
- package/util/layouts/GranularRectLayout.js +388 -555
- package/util/layouts/MultiLayout.js +41 -109
- package/util/layouts/PrecomputedLayout.js +56 -112
- package/util/layouts/PrecomputedMultiLayout.js +22 -59
- package/util/layouts/SceneGraph.js +127 -197
- package/util/layouts/index.js +29 -66
- package/util/mst-reflection.js +55 -71
- package/util/offscreenCanvasPonyfill.js +66 -134
- package/util/offscreenCanvasUtils.d.ts +2 -7
- package/util/offscreenCanvasUtils.js +49 -146
- package/util/range.js +29 -40
- package/util/rxjs.js +20 -27
- package/util/simpleFeature.js +88 -152
- package/util/stats.js +91 -151
- package/util/tracks.js +130 -173
- package/util/types/index.js +110 -179
- package/util/types/mst.js +91 -146
- package/util/types/util.js +1 -4
- package/util/when.js +54 -101
- package/BaseFeatureWidget/SequenceFeatureDetails.test.js +0 -122
- package/BaseFeatureWidget/index.test.js +0 -69
- package/TextSearch/BaseResults.test.js +0 -42
- package/configuration/configurationSchema.test.js +0 -266
- package/configuration/configurationSlot.test.js +0 -69
- package/configuration/util.test.js +0 -39
- package/data_adapters/BaseAdapter.test.js +0 -200
- package/declare.d.js +0 -1
- package/pluggableElementTypes/RpcMethodType.test.js +0 -118
- package/pluggableElementTypes/renderers/declare.d.js +0 -1
- package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +0 -20
- package/rpc/BaseRpcDriver.test.js +0 -540
- package/rpc/declaration.d.js +0 -1
- package/ui/FatalErrorDialog.test.js +0 -82
- package/ui/SanitizedHTML.test.js +0 -36
- package/ui/theme.test.js +0 -92
- package/util/Base1DViewModel.test.js +0 -130
- package/util/calculateDynamicBlocks.test.js +0 -74
- package/util/calculateStaticBlocks.test.js +0 -297
- package/util/declare.d.js +0 -1
- package/util/formatFastaStrings.test.js +0 -40
- package/util/index.test.js +0 -213
- package/util/jexlStrings.test.js +0 -48
- package/util/layouts/GranularRectLayout.test.js +0 -99
- package/util/range.test.js +0 -64
- package/util/simpleFeature.test.js +0 -34
- package/util/stats.test.js +0 -172
package/ui/theme.js
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Object.defineProperty(exports, "__esModule", {
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var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.createJBrowseTheme = exports.jbrowseBaseTheme = exports.createJBrowseDefaultOverrides = exports.createJBrowseDefaultProps = exports.jbrowseDefaultPalette = void 0;
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const colors_1 = require("@mui/material/colors");
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const styles_1 = require("@mui/material/styles");
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const deepmerge_1 = __importDefault(require("deepmerge"));
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const midnight = '#0D233F';
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const grape = '#721E63';
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const forest = '#135560';
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const mandarin = '#FFB11D';
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const refTheme = (0, styles_1.createTheme)();
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exports.jbrowseDefaultPalette = {
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// type: 'dark',
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primary: { main: midnight },
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secondary: { main: grape },
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tertiary: refTheme.palette.augmentColor({ color: { main: forest } }),
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quaternary: refTheme.palette.augmentColor({ color: { main: mandarin } }),
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stopCodon: '#e22',
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startCodon: '#3e3',
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bases: {
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A: refTheme.palette.augmentColor({ color: colors_1.green }),
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C: refTheme.palette.augmentColor({ color: colors_1.blue }),
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G: refTheme.palette.augmentColor({ color: colors_1.amber }),
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T: refTheme.palette.augmentColor({ color: colors_1.red }),
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},
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};
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function createJBrowseDefaultProps( /* palette: PaletteOptions = {} */) {
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return {
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components: {
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MuiButton: {
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defaultProps: {
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size: 'small',
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},
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},
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MuiAccordion: {
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defaultProps: {
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disableGutters: true,
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TransitionProps: { timeout: 150 },
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},
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},
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MuiFilledInput: {
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defaultProps: {
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margin: 'dense',
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MuiFormControl: {
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defaultProps: {
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margin: 'dense',
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size: 'small',
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},
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},
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MuiFormHelperText: {
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defaultProps: {
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margin: 'dense',
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},
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},
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MuiIconButton: {
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defaultProps: {
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size: 'small',
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},
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},
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MuiInputBase: {
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defaultProps: {
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margin: 'dense',
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},
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MuiAutocomplete: {
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defaultProps: {
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size: 'small',
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},
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},
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MuiInputLabel: {
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defaultProps: {
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margin: 'dense',
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},
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},
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MuiToolbar: {
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defaultProps: {
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variant: 'dense',
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},
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},
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MuiListItem: {
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defaultProps: {
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dense: true,
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},
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MuiOutlinedInput: {
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defaultProps: {
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margin: 'dense',
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},
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MuiFab: {
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defaultProps: {
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size: 'small',
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},
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MuiTable: {
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defaultProps: {
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size: 'small',
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MuiMenuList: {
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defaultProps: {
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dense: true,
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MuiMenuItem: {
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defaultProps: {
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dense: true,
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},
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},
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MuiTextField: {
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defaultProps: {
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margin: 'dense',
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variant: 'standard',
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exports.createJBrowseDefaultProps = createJBrowseDefaultProps;
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function createJBrowseDefaultOverrides(palette = {}) {
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const generatedPalette = (0, deepmerge_1.default)(exports.jbrowseDefaultPalette, palette);
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return {
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components: {
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MuiIconButton: {
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styleOverrides: {
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colorSecondary: {
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color: generatedPalette.tertiary.main,
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MuiButton: {
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styleOverrides: {
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textSecondary: {
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color: generatedPalette.tertiary.main,
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MuiFab: {
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styleOverrides: {
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secondary: {
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backgroundColor: generatedPalette.quaternary.main,
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},
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},
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MuiLink: {
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styleOverrides: {
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root: {
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color: generatedPalette.tertiary.main,
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},
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MuiAccordionSummary: {
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styleOverrides: {
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root: {
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backgroundColor: generatedPalette.tertiary.main,
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},
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content: {
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color: generatedPalette.tertiary.contrastText,
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},
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};
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}
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exports.createJBrowseDefaultOverrides = createJBrowseDefaultOverrides;
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exports.jbrowseBaseTheme = {
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palette: exports.jbrowseDefaultPalette,
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typography: { fontSize: 12 },
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+
spacing: 4,
|
|
175
|
+
...(0, deepmerge_1.default)(createJBrowseDefaultProps(), createJBrowseDefaultOverrides()),
|
|
64
176
|
};
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
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71
|
-
|
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72
|
-
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73
|
-
|
|
74
|
-
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75
|
-
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76
|
-
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77
|
-
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78
|
-
defaultProps: {
|
|
79
|
-
disableGutters: true,
|
|
80
|
-
TransitionProps: {
|
|
81
|
-
timeout: 150
|
|
82
|
-
}
|
|
83
|
-
}
|
|
84
|
-
},
|
|
85
|
-
MuiFilledInput: {
|
|
86
|
-
defaultProps: {
|
|
87
|
-
margin: 'dense'
|
|
88
|
-
}
|
|
89
|
-
},
|
|
90
|
-
MuiFormControl: {
|
|
91
|
-
defaultProps: {
|
|
92
|
-
margin: 'dense',
|
|
93
|
-
size: 'small'
|
|
94
|
-
}
|
|
95
|
-
},
|
|
96
|
-
MuiFormHelperText: {
|
|
97
|
-
defaultProps: {
|
|
98
|
-
margin: 'dense'
|
|
99
|
-
}
|
|
100
|
-
},
|
|
101
|
-
MuiIconButton: {
|
|
102
|
-
defaultProps: {
|
|
103
|
-
size: 'small'
|
|
104
|
-
}
|
|
105
|
-
},
|
|
106
|
-
MuiInputBase: {
|
|
107
|
-
defaultProps: {
|
|
108
|
-
margin: 'dense'
|
|
109
|
-
}
|
|
110
|
-
},
|
|
111
|
-
MuiAutocomplete: {
|
|
112
|
-
defaultProps: {
|
|
113
|
-
size: 'small'
|
|
114
|
-
}
|
|
115
|
-
},
|
|
116
|
-
MuiInputLabel: {
|
|
117
|
-
defaultProps: {
|
|
118
|
-
margin: 'dense'
|
|
119
|
-
}
|
|
120
|
-
},
|
|
121
|
-
MuiToolbar: {
|
|
122
|
-
defaultProps: {
|
|
123
|
-
variant: 'dense'
|
|
124
|
-
}
|
|
125
|
-
},
|
|
126
|
-
MuiListItem: {
|
|
127
|
-
defaultProps: {
|
|
128
|
-
dense: true
|
|
129
|
-
}
|
|
130
|
-
},
|
|
131
|
-
MuiOutlinedInput: {
|
|
132
|
-
defaultProps: {
|
|
133
|
-
margin: 'dense'
|
|
134
|
-
}
|
|
135
|
-
},
|
|
136
|
-
MuiFab: {
|
|
137
|
-
defaultProps: {
|
|
138
|
-
size: 'small'
|
|
139
|
-
}
|
|
140
|
-
},
|
|
141
|
-
MuiTable: {
|
|
142
|
-
defaultProps: {
|
|
143
|
-
size: 'small'
|
|
144
|
-
}
|
|
145
|
-
},
|
|
146
|
-
MuiMenuList: {
|
|
147
|
-
defaultProps: {
|
|
148
|
-
dense: true
|
|
149
|
-
}
|
|
150
|
-
},
|
|
151
|
-
MuiMenuItem: {
|
|
152
|
-
defaultProps: {
|
|
153
|
-
dense: true
|
|
154
|
-
}
|
|
155
|
-
},
|
|
156
|
-
MuiTextField: {
|
|
157
|
-
defaultProps: {
|
|
158
|
-
margin: 'dense',
|
|
159
|
-
variant: 'standard'
|
|
160
|
-
}
|
|
161
|
-
}
|
|
177
|
+
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
178
|
+
function createJBrowseTheme(theme) {
|
|
179
|
+
var _a, _b, _c, _d;
|
|
180
|
+
if ((_a = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _a === void 0 ? void 0 : _a.tertiary) {
|
|
181
|
+
theme = (0, deepmerge_1.default)(theme, {
|
|
182
|
+
palette: {
|
|
183
|
+
tertiary: refTheme.palette.augmentColor(((_b = theme.palette.tertiary) === null || _b === void 0 ? void 0 : _b.color)
|
|
184
|
+
? theme.palette.tertiary
|
|
185
|
+
: {
|
|
186
|
+
color: theme.palette.tertiary,
|
|
187
|
+
}),
|
|
188
|
+
},
|
|
189
|
+
});
|
|
162
190
|
}
|
|
163
|
-
|
|
164
|
-
|
|
165
|
-
|
|
166
|
-
|
|
167
|
-
|
|
168
|
-
|
|
169
|
-
|
|
170
|
-
|
|
171
|
-
|
|
172
|
-
|
|
173
|
-
colorSecondary: {
|
|
174
|
-
color: generatedPalette.tertiary.main
|
|
175
|
-
}
|
|
176
|
-
}
|
|
177
|
-
},
|
|
178
|
-
MuiButton: {
|
|
179
|
-
styleOverrides: {
|
|
180
|
-
textSecondary: {
|
|
181
|
-
color: generatedPalette.tertiary.main
|
|
182
|
-
}
|
|
183
|
-
}
|
|
184
|
-
},
|
|
185
|
-
MuiFab: {
|
|
186
|
-
styleOverrides: {
|
|
187
|
-
secondary: {
|
|
188
|
-
backgroundColor: generatedPalette.quaternary.main
|
|
189
|
-
}
|
|
190
|
-
}
|
|
191
|
-
},
|
|
192
|
-
MuiLink: {
|
|
193
|
-
styleOverrides: {
|
|
194
|
-
root: {
|
|
195
|
-
color: generatedPalette.tertiary.main
|
|
196
|
-
}
|
|
197
|
-
}
|
|
198
|
-
},
|
|
199
|
-
MuiAccordionSummary: {
|
|
200
|
-
styleOverrides: {
|
|
201
|
-
root: {
|
|
202
|
-
backgroundColor: generatedPalette.tertiary.main
|
|
203
|
-
},
|
|
204
|
-
content: {
|
|
205
|
-
color: generatedPalette.tertiary.contrastText
|
|
206
|
-
}
|
|
207
|
-
}
|
|
208
|
-
}
|
|
191
|
+
if ((_c = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _c === void 0 ? void 0 : _c.quaternary) {
|
|
192
|
+
theme = (0, deepmerge_1.default)(theme, {
|
|
193
|
+
palette: {
|
|
194
|
+
quaternary: refTheme.palette.augmentColor(((_d = theme.palette.quaternary) === null || _d === void 0 ? void 0 : _d.color)
|
|
195
|
+
? theme.palette.quaternary
|
|
196
|
+
: {
|
|
197
|
+
color: theme.palette.quaternary,
|
|
198
|
+
}),
|
|
199
|
+
},
|
|
200
|
+
});
|
|
209
201
|
}
|
|
210
|
-
|
|
202
|
+
// @ts-ignore
|
|
203
|
+
return (0, styles_1.createTheme)((0, deepmerge_1.default)(exports.jbrowseBaseTheme, theme || {}));
|
|
211
204
|
}
|
|
212
|
-
|
|
213
|
-
var jbrowseBaseTheme = _objectSpread({
|
|
214
|
-
palette: jbrowseDefaultPalette,
|
|
215
|
-
typography: {
|
|
216
|
-
fontSize: 12
|
|
217
|
-
},
|
|
218
|
-
spacing: 4
|
|
219
|
-
}, (0, _deepmerge.default)(createJBrowseDefaultProps(), createJBrowseDefaultOverrides())); // eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
220
|
-
|
|
221
|
-
|
|
222
|
-
exports.jbrowseBaseTheme = jbrowseBaseTheme;
|
|
223
|
-
|
|
224
|
-
function createJBrowseTheme(theme) {
|
|
225
|
-
var _theme, _theme$palette, _theme2, _theme2$palette;
|
|
226
|
-
|
|
227
|
-
if ((_theme = theme) !== null && _theme !== void 0 && (_theme$palette = _theme.palette) !== null && _theme$palette !== void 0 && _theme$palette.tertiary) {
|
|
228
|
-
var _theme$palette$tertia;
|
|
229
|
-
|
|
230
|
-
theme = (0, _deepmerge.default)(theme, {
|
|
231
|
-
palette: {
|
|
232
|
-
tertiary: refTheme.palette.augmentColor((_theme$palette$tertia = theme.palette.tertiary) !== null && _theme$palette$tertia !== void 0 && _theme$palette$tertia.color ? theme.palette.tertiary : {
|
|
233
|
-
color: theme.palette.tertiary
|
|
234
|
-
})
|
|
235
|
-
}
|
|
236
|
-
});
|
|
237
|
-
}
|
|
238
|
-
|
|
239
|
-
if ((_theme2 = theme) !== null && _theme2 !== void 0 && (_theme2$palette = _theme2.palette) !== null && _theme2$palette !== void 0 && _theme2$palette.quaternary) {
|
|
240
|
-
var _theme$palette$quater;
|
|
241
|
-
|
|
242
|
-
theme = (0, _deepmerge.default)(theme, {
|
|
243
|
-
palette: {
|
|
244
|
-
quaternary: refTheme.palette.augmentColor((_theme$palette$quater = theme.palette.quaternary) !== null && _theme$palette$quater !== void 0 && _theme$palette$quater.color ? theme.palette.quaternary : {
|
|
245
|
-
color: theme.palette.quaternary
|
|
246
|
-
})
|
|
247
|
-
}
|
|
248
|
-
});
|
|
249
|
-
} // @ts-ignore
|
|
250
|
-
|
|
251
|
-
|
|
252
|
-
return (0, _styles.createTheme)((0, _deepmerge.default)(jbrowseBaseTheme, theme || {}));
|
|
253
|
-
}
|
|
205
|
+
exports.createJBrowseTheme = createJBrowseTheme;
|