@jbrowse/core 1.7.11 → 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 +20 -4
- package/BaseFeatureWidget/BaseFeatureDetail.js +313 -558
- package/BaseFeatureWidget/SequenceFeatureDetails.js +213 -473
- package/BaseFeatureWidget/index.d.ts +2 -2
- package/BaseFeatureWidget/index.js +88 -124
- package/BaseFeatureWidget/types.d.ts +1 -0
- 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 +84 -117
- package/PluginManager.js +377 -666
- package/ReExports/Attributes.d.ts +2 -0
- package/ReExports/Attributes.js +5 -0
- package/ReExports/BaseCard.d.ts +2 -0
- package/ReExports/BaseCard.js +5 -0
- package/ReExports/DataGrid.d.ts +2 -0
- package/ReExports/DataGrid.js +6 -0
- package/ReExports/FeatureDetails.d.ts +2 -0
- package/ReExports/FeatureDetails.js +5 -0
- package/ReExports/index.js +6 -12
- package/ReExports/list.d.ts +5 -0
- package/ReExports/list.js +271 -7
- package/ReExports/material-ui-colors.d.ts +1 -19
- package/ReExports/material-ui-colors.js +16 -158
- package/ReExports/modules.d.ts +68 -109
- package/ReExports/modules.js +455 -244
- package/TextSearch/BaseResults.js +51 -123
- package/TextSearch/TextSearchManager.d.ts +3 -1
- package/TextSearch/TextSearchManager.js +66 -144
- package/assemblyManager/assembly.js +280 -554
- package/assemblyManager/assemblyConfigSchema.js +47 -64
- package/assemblyManager/assemblyManager.d.ts +12 -10
- package/assemblyManager/assemblyManager.js +126 -270
- 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.d.ts +1 -1
- 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 +16 -18
- 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.d.ts +10 -10
- package/pluggableElementTypes/models/BaseDisplayModel.js +58 -95
- package/pluggableElementTypes/models/BaseTrackModel.d.ts +1 -1
- package/pluggableElementTypes/models/BaseTrackModel.js +139 -200
- 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 -255
- package/pluggableElementTypes/renderers/RendererType.js +31 -105
- package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +61 -72
- package/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +2 -2
- 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.d.ts +1 -3
- package/rpc/coreRpcMethods.js +221 -959
- package/rpc/remoteAbortSignals.js +46 -70
- package/tsconfig.build.tsbuildinfo +1 -1
- package/ui/AboutDialog.js +107 -158
- package/ui/App.js +157 -261
- package/ui/AssemblySelector.d.ts +1 -1
- package/ui/AssemblySelector.js +59 -115
- package/ui/CascadingMenu.js +100 -199
- package/ui/ColorPicker.d.ts +16 -0
- package/ui/ColorPicker.js +97 -0
- package/ui/Drawer.js +28 -58
- package/ui/DrawerWidget.js +109 -209
- package/ui/DropDownMenu.d.ts +0 -8
- package/ui/DropDownMenu.js +60 -97
- package/ui/EditableTypography.d.ts +1 -1
- package/ui/EditableTypography.js +87 -155
- package/ui/ErrorMessage.js +41 -66
- 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 -71
- package/ui/FileSelector/UrlChooser.js +17 -38
- package/ui/FileSelector/index.js +6 -12
- package/ui/Icons.d.ts +1 -1
- package/ui/Icons.js +45 -69
- package/ui/Logo.js +57 -110
- package/ui/Menu.d.ts +1 -1
- package/ui/Menu.js +232 -355
- package/ui/PrerenderedCanvas.js +63 -78
- package/ui/ResizeHandle.js +87 -114
- package/ui/ReturnToImportFormDialog.js +32 -59
- package/ui/SanitizedHTML.js +63 -52
- package/ui/Snackbar.js +74 -99
- package/ui/SnackbarModel.js +37 -51
- package/ui/Tooltip.d.ts +3 -1
- package/ui/Tooltip.js +49 -74
- package/ui/ViewContainer.js +113 -183
- 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.d.ts +279 -131
- package/ui/theme.js +197 -225
- package/util/Base1DUtils.d.ts +32 -0
- package/util/Base1DUtils.js +174 -0
- package/util/Base1DViewModel.d.ts +16 -37
- package/util/Base1DViewModel.js +116 -295
- 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 +18 -39
- package/util/index.js +743 -1236
- 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 -557
- package/util/layouts/MultiLayout.js +41 -109
- package/util/layouts/PrecomputedLayout.js +56 -114
- 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 -171
- package/util/types/index.d.ts +3 -3
- package/util/types/index.js +110 -179
- package/util/types/mst.d.ts +3 -3
- package/util/types/mst.js +91 -142
- 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 -51
- 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 -111
- 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/util/index.d.ts
CHANGED
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@@ -1,7 +1,8 @@
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-
import { IAnyStateTreeNode } from 'mobx-state-tree';
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import { IAnyStateTreeNode, IStateTreeNode } from 'mobx-state-tree';
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import { IReactionPublic, IReactionOptions } from 'mobx';
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import SimpleFeature, { Feature, isFeature } from './simpleFeature';
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import { AssemblyManager, Region, TypeTestedByPredicate } from './types';
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import { BaseBlock } from './blockTypes';
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export type { Feature };
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export * from './types';
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export * from './aborting';
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@@ -149,33 +150,7 @@ export declare function bpSpanPx(leftBp: number, rightBp: number, region: {
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end: number;
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reversed?: boolean;
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}, bpPerPx: number): [number, number];
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export declare const objectFromEntries: {
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<T = any>(entries: Iterable<readonly [PropertyKey, T]>): {
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[k: string]: T;
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};
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(entries: Iterable<readonly any[]>): any;
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};
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export declare function iterMap<T, U>(iterable: Iterable<T>, func: (item: T) => U, sizeHint?: number): U[];
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interface Assembly {
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name: string;
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[key: string]: any;
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}
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interface Track {
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trackId: string;
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[key: string]: any;
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}
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interface Config {
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savedSessions: unknown[];
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assemblies: Assembly[];
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tracks: Track[];
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defaultSession?: {};
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}
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export declare function mergeConfigs(A: Config, B: Config): {
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savedSessions: unknown[];
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assemblies: Assembly[];
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tracks: Track[];
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defaultSession: {};
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};
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/**
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* Returns the index of the last element in the array where predicate is true,
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* and -1 otherwise.
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@@ -222,7 +197,7 @@ export declare function renameRegionsIfNeeded<ARGTYPE extends {
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export declare function minmax(a: number, b: number): number[];
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export declare function stringify({ refName, coord, oob, }: {
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coord: number;
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refName
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refName?: string;
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oob?: boolean;
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}): string;
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export declare const isElectron: boolean;
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interRegionPaddingWidth: number;
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minimumBlockWidth: number;
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width: number;
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offsetPx: number;
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staticBlocks: {
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contentBlocks: BaseBlock[];
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blocks: BaseBlock[];
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};
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displayedRegions: (IStateTreeNode & {
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start: number;
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end: number;
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refName: string;
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reversed: boolean;
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assemblyName: string;
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})[];
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};
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export declare function viewBpToPx({ refName, coord, regionNumber, self, }: {
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refName: string;
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coord: number;
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regionNumber?: number;
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self: ViewSnap;
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}): {
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index: number;
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offsetPx: number;
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} | undefined;
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export declare function supportedIndexingAdapters(type: string): boolean;
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export declare function getBpDisplayStr(totalBp: number): string;
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export declare function toLocale(n: number): string;
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sessionId: string;
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layoutId: string;
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}): string;
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export declare const useLocalStorage: (key: string, defaultValue?: string) => [string, (arg: string) => void];
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export declare function getUriLink(value: {
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uri: string;
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baseUri?: string;
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}): string;
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export declare function getStr(obj: unknown): string;
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export declare function measureGridWidth(elements: string[]): number;
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