@jbrowse/plugin-linear-genome-view 1.6.9 → 1.7.3
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/dist/BaseLinearDisplay/components/BaseLinearDisplay.d.ts +13 -13
- package/dist/BaseLinearDisplay/components/BaseLinearDisplay.js +232 -0
- package/dist/BaseLinearDisplay/components/Block.d.ts +15 -15
- package/dist/BaseLinearDisplay/components/Block.js +86 -0
- package/dist/BaseLinearDisplay/components/LinearBlocks.d.ts +12 -12
- package/dist/BaseLinearDisplay/components/LinearBlocks.js +110 -0
- package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.d.ts +4 -4
- package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js +192 -0
- package/dist/BaseLinearDisplay/index.d.ts +5 -5
- package/dist/BaseLinearDisplay/index.js +41 -0
- package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +227 -230
- package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js +763 -0
- package/dist/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.d.ts +1 -1
- package/dist/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.js +24 -0
- package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts +96 -96
- package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js +328 -0
- package/dist/LinearBareDisplay/configSchema.d.ts +2 -2
- package/dist/LinearBareDisplay/configSchema.js +19 -0
- package/dist/LinearBareDisplay/index.d.ts +2 -2
- package/dist/LinearBareDisplay/index.js +21 -0
- package/dist/LinearBareDisplay/index.test.js +33 -0
- package/dist/LinearBareDisplay/model.d.ts +192 -192
- package/dist/LinearBareDisplay/model.js +44 -0
- package/dist/LinearBasicDisplay/components/SetMaxHeight.d.ts +10 -10
- package/dist/LinearBasicDisplay/components/SetMaxHeight.js +94 -0
- package/dist/LinearBasicDisplay/configSchema.d.ts +2 -2
- package/dist/LinearBasicDisplay/configSchema.js +25 -0
- package/dist/LinearBasicDisplay/index.d.ts +2 -2
- package/dist/LinearBasicDisplay/index.js +23 -0
- package/dist/LinearBasicDisplay/model.d.ts +213 -213
- package/dist/LinearBasicDisplay/model.js +162 -0
- package/dist/LinearGenomeView/components/CenterLine.d.ts +14 -14
- package/dist/LinearGenomeView/components/CenterLine.js +80 -0
- package/dist/LinearGenomeView/components/ExportSvgDialog.d.ts +6 -6
- package/dist/LinearGenomeView/components/ExportSvgDialog.js +137 -0
- package/dist/LinearGenomeView/components/Header.d.ts +7 -7
- package/dist/LinearGenomeView/components/Header.js +144 -0
- package/dist/LinearGenomeView/components/HelpDialog.d.ts +5 -5
- package/dist/LinearGenomeView/components/HelpDialog.js +48 -0
- package/dist/LinearGenomeView/components/ImportForm.d.ts +7 -7
- package/dist/LinearGenomeView/components/ImportForm.js +330 -0
- package/dist/LinearGenomeView/components/LinearGenomeView.d.ts +7 -7
- package/dist/LinearGenomeView/components/LinearGenomeView.js +129 -0
- package/dist/LinearGenomeView/components/LinearGenomeView.test.js +234 -0
- package/dist/LinearGenomeView/components/LinearGenomeViewSvg.d.ts +4 -4
- package/dist/LinearGenomeView/components/LinearGenomeViewSvg.js +349 -0
- package/dist/LinearGenomeView/components/MiniControls.d.ts +6 -6
- package/dist/LinearGenomeView/components/MiniControls.js +83 -0
- package/dist/LinearGenomeView/components/OverviewRubberBand.d.ts +22 -22
- package/dist/LinearGenomeView/components/OverviewRubberBand.js +310 -0
- package/dist/LinearGenomeView/components/OverviewScaleBar.d.ts +132 -124
- package/dist/LinearGenomeView/components/OverviewScaleBar.js +403 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete.d.ts +21 -21
- package/dist/LinearGenomeView/components/RefNameAutocomplete.js +331 -0
- package/dist/LinearGenomeView/components/RubberBand.d.ts +9 -20
- package/dist/LinearGenomeView/components/RubberBand.js +309 -0
- package/dist/LinearGenomeView/components/Ruler.d.ts +27 -27
- package/dist/LinearGenomeView/components/Ruler.js +101 -0
- package/dist/LinearGenomeView/components/ScaleBar.d.ts +401 -401
- package/dist/LinearGenomeView/components/ScaleBar.js +184 -0
- package/dist/LinearGenomeView/components/ScaleBar.test.js +180 -0
- package/dist/LinearGenomeView/components/SearchBox.d.ts +8 -8
- package/dist/LinearGenomeView/components/SearchBox.js +201 -0
- package/dist/LinearGenomeView/components/SearchResultsDialog.d.ts +8 -8
- package/dist/LinearGenomeView/components/SearchResultsDialog.js +159 -0
- package/dist/LinearGenomeView/components/SequenceDialog.d.ts +8 -8
- package/dist/LinearGenomeView/components/SequenceDialog.js +304 -0
- package/dist/LinearGenomeView/components/TrackContainer.d.ts +9 -9
- package/dist/LinearGenomeView/components/TrackContainer.js +179 -0
- package/dist/LinearGenomeView/components/TrackLabel.d.ts +44 -44
- package/dist/LinearGenomeView/components/TrackLabel.js +165 -0
- package/dist/LinearGenomeView/components/TracksContainer.d.ts +10 -10
- package/dist/LinearGenomeView/components/TracksContainer.js +214 -0
- package/dist/LinearGenomeView/components/VerticalGuides.d.ts +9 -9
- package/dist/LinearGenomeView/components/VerticalGuides.js +116 -0
- package/dist/LinearGenomeView/components/ZoomControls.d.ts +7 -7
- package/dist/LinearGenomeView/components/ZoomControls.js +92 -0
- package/dist/LinearGenomeView/components/util.d.ts +2 -2
- package/dist/LinearGenomeView/components/util.js +16 -0
- package/dist/LinearGenomeView/index.d.ts +292 -292
- package/dist/LinearGenomeView/index.js +1418 -0
- package/dist/LinearGenomeView/index.test.js +1170 -0
- package/dist/LinearGenomeView/util.d.ts +14 -14
- package/dist/LinearGenomeView/util.js +93 -0
- package/dist/LinearGenomeView/util.test.js +78 -0
- package/dist/index.d.ts +565 -565
- package/dist/index.js +293 -6
- package/package.json +6 -9
- package/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx +2 -0
- package/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts +10 -8
- package/src/LinearBasicDisplay/components/SetMaxHeight.tsx +1 -1
- package/src/LinearBasicDisplay/model.ts +17 -18
- package/src/LinearGenomeView/components/Header.tsx +1 -1
- package/src/LinearGenomeView/components/ImportForm.tsx +10 -4
- package/src/LinearGenomeView/components/LinearGenomeView.test.js +1 -0
- package/src/LinearGenomeView/components/OverviewScaleBar.tsx +2 -2
- package/src/LinearGenomeView/components/RubberBand.tsx +14 -24
- package/src/LinearGenomeView/components/ScaleBar.test.tsx +1 -0
- package/src/LinearGenomeView/components/ScaleBar.tsx +3 -6
- package/src/LinearGenomeView/components/SequenceDialog.tsx +1 -1
- package/src/LinearGenomeView/components/TrackLabel.tsx +1 -1
- package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.js.snap +0 -4
- package/src/LinearGenomeView/index.tsx +2 -3
- package/dist/LinearBareDisplay/index.test.d.ts +0 -1
- package/dist/LinearGenomeView/components/LinearGenomeView.test.d.ts +0 -1
- package/dist/plugin-linear-genome-view.cjs.development.js +0 -8121
- package/dist/plugin-linear-genome-view.cjs.development.js.map +0 -1
- package/dist/plugin-linear-genome-view.cjs.production.min.js +0 -2
- package/dist/plugin-linear-genome-view.cjs.production.min.js.map +0 -1
- package/dist/plugin-linear-genome-view.esm.js +0 -8105
- package/dist/plugin-linear-genome-view.esm.js.map +0 -1
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import {
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import {
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import {
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declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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type: import("mobx-state-tree").ISimpleType<string>;
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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} & {
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height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
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blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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key: import("mobx-state-tree").ISimpleType<string>;
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region: import("mobx-state-tree").IModelType<{
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refName: import("mobx-state-tree").ISimpleType<string>;
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start: import("mobx-state-tree").ISimpleType<number>;
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end: import("mobx-state-tree").ISimpleType<number>;
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reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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assemblyName: import("mobx-state-tree").ISimpleType<string>;
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setRefName(newRefName: string): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
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reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
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isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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renderInProgress: AbortController | undefined;
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reactElement: import("react").ReactElement<any, string |
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features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
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status: string;
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message: string | undefined;
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doReload(): void;
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setStatus(message: string): void;
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setLoading(abortController: AbortController): void;
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setMessage(messageText: string): void;
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features: Map<string, import("@jbrowse/core/util").Feature>;
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layout: any;
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maxHeightReached: boolean;
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renderProps: any;
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setError(error: unknown): void;
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reload(): void;
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beforeDestroy(): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
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trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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readonly DisplayBlurb: import("react").FC<{
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model: import("mobx-state-tree").ModelInstanceTypeProps<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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trackMenuItems(): MenuItem[];
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readonly viewMenuActions: MenuItem[];
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regionCannotBeRendered(): undefined;
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setError(error?: unknown): void;
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setRpcDriverName(rpcDriverName: string): void;
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currBpPerPx: number;
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message: string;
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featureIdUnderMouse: string | undefined;
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contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
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scrollTop: number;
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estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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readonly renderDelay: number;
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readonly TooltipComponent: import("react").FC<any>;
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readonly selectedFeatureId: string | undefined;
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readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
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readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
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getFeatureOverlapping(blockKey: string, x: number, y: number): any;
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getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
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readonly maxAllowableBytes: number;
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afterAttach(): void;
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estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
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signal?: AbortSignal | undefined;
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updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
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addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
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setCurrBpPerPx(n: number): void;
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deleteBlock(key: string): void;
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selectFeature(feature: import("@jbrowse/core/util").Feature): void;
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setFeatureIdUnderMouse(feature: string | undefined): void;
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reload(): void;
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setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
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readonly regionTooLargeReason: string;
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} & {
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regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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label: string;
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icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
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onClick: () => void;
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}[];
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renderProps(): any;
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} & {
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renderSvg(opts: import("../LinearGenomeView").ExportSvgOptions & {
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overrideHeight: number;
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}): Promise<JSX.Element>;
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} & {
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readonly rendererTypeName: any;
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readonly showLabels: any;
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readonly showDescriptions: any;
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readonly maxHeight: any;
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readonly displayMode: any;
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readonly rendererConfig: any;
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} & {
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toggleShowLabels(): void;
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toggleShowDescriptions(): void;
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setDisplayMode(val: string): void;
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setMaxHeight(val: number): void;
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} & {
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renderProps(): any;
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trackMenuItems(): MenuItem[];
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}, import("mobx-state-tree")._NotCustomized, {
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id: string;
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type: string;
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rpcDriverName: string | undefined;
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height: number;
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userBpPerPxLimit: number | undefined;
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userByteSizeLimit: number | undefined;
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} & import("mobx-state-tree")._NotCustomized>;
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export declare type FeatureTrackStateModel = ReturnType<typeof stateModelFactory>;
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export declare type FeatureTrackModel = Instance<FeatureTrackStateModel>;
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export default stateModelFactory;
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1
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+
/// <reference types="react" />
|
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2
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+
import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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|
+
import { MenuItem } from '@jbrowse/core/ui';
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+
import { Instance } from 'mobx-state-tree';
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|
+
declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
|
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|
+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
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7
|
+
type: import("mobx-state-tree").ISimpleType<string>;
|
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
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|
+
} & {
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|
+
height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
|
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|
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blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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key: import("mobx-state-tree").ISimpleType<string>;
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region: import("mobx-state-tree").IModelType<{
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refName: import("mobx-state-tree").ISimpleType<string>;
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|
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start: import("mobx-state-tree").ISimpleType<number>;
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|
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end: import("mobx-state-tree").ISimpleType<number>;
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reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
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|
+
} & {
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|
+
assemblyName: import("mobx-state-tree").ISimpleType<string>;
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}, {
|
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|
+
setRefName(newRefName: string): void;
|
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|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
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|
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reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
|
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|
+
isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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|
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isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
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|
+
}, {
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|
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renderInProgress: AbortController | undefined;
|
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|
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filled: boolean;
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|
+
reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
|
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|
+
features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
|
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|
+
layout: any;
|
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|
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status: string;
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33
|
+
error: unknown;
|
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34
|
+
message: string | undefined;
|
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35
|
+
maxHeightReached: boolean;
|
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36
|
+
ReactComponent: ({ model, }: {
|
|
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|
+
model: any;
|
|
38
|
+
}) => any;
|
|
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|
+
renderProps: any;
|
|
40
|
+
} & {
|
|
41
|
+
doReload(): void;
|
|
42
|
+
afterAttach(): void;
|
|
43
|
+
setStatus(message: string): void;
|
|
44
|
+
setLoading(abortController: AbortController): void;
|
|
45
|
+
setMessage(messageText: string): void;
|
|
46
|
+
setRendered(props: {
|
|
47
|
+
reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
|
|
48
|
+
features: Map<string, import("@jbrowse/core/util").Feature>;
|
|
49
|
+
layout: any;
|
|
50
|
+
maxHeightReached: boolean;
|
|
51
|
+
renderProps: any;
|
|
52
|
+
} | undefined): void;
|
|
53
|
+
setError(error: unknown): void;
|
|
54
|
+
reload(): void;
|
|
55
|
+
beforeDestroy(): void;
|
|
56
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
57
|
+
userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
58
|
+
userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
59
|
+
} & {
|
|
60
|
+
type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
|
|
61
|
+
trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
|
|
62
|
+
trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
|
|
63
|
+
trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
64
|
+
trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
65
|
+
configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
|
|
66
|
+
}, {
|
|
67
|
+
rendererTypeName: string;
|
|
68
|
+
error: unknown;
|
|
69
|
+
} & {
|
|
70
|
+
readonly RenderingComponent: import("react").FC<{
|
|
71
|
+
model: import("mobx-state-tree").ModelInstanceTypeProps<{
|
|
72
|
+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
73
|
+
type: import("mobx-state-tree").ISimpleType<string>;
|
|
74
|
+
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
75
|
+
}> & {
|
|
76
|
+
rendererTypeName: string;
|
|
77
|
+
error: unknown;
|
|
78
|
+
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
79
|
+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
80
|
+
type: import("mobx-state-tree").ISimpleType<string>;
|
|
81
|
+
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
82
|
+
}, {
|
|
83
|
+
rendererTypeName: string;
|
|
84
|
+
error: unknown;
|
|
85
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
86
|
+
onHorizontalScroll?: Function | undefined;
|
|
87
|
+
blockState?: Record<string, any> | undefined;
|
|
88
|
+
}>;
|
|
89
|
+
readonly DisplayBlurb: import("react").FC<{
|
|
90
|
+
model: import("mobx-state-tree").ModelInstanceTypeProps<{
|
|
91
|
+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
92
|
+
type: import("mobx-state-tree").ISimpleType<string>;
|
|
93
|
+
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
94
|
+
}> & {
|
|
95
|
+
rendererTypeName: string;
|
|
96
|
+
error: unknown;
|
|
97
|
+
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
98
|
+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
99
|
+
type: import("mobx-state-tree").ISimpleType<string>;
|
|
100
|
+
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
101
|
+
}, {
|
|
102
|
+
rendererTypeName: string;
|
|
103
|
+
error: unknown;
|
|
104
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
105
|
+
}> | null;
|
|
106
|
+
readonly adapterConfig: any;
|
|
107
|
+
readonly parentTrack: any;
|
|
108
|
+
renderProps(): any;
|
|
109
|
+
readonly rendererType: any;
|
|
110
|
+
readonly DisplayMessageComponent: import("react").FC<any> | undefined;
|
|
111
|
+
trackMenuItems(): MenuItem[];
|
|
112
|
+
readonly viewMenuActions: MenuItem[];
|
|
113
|
+
regionCannotBeRendered(): undefined;
|
|
114
|
+
} & {
|
|
115
|
+
setError(error?: unknown): void;
|
|
116
|
+
setRpcDriverName(rpcDriverName: string): void;
|
|
117
|
+
reload(): void;
|
|
118
|
+
} & {
|
|
119
|
+
currBpPerPx: number;
|
|
120
|
+
message: string;
|
|
121
|
+
featureIdUnderMouse: string | undefined;
|
|
122
|
+
contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
|
|
123
|
+
scrollTop: number;
|
|
124
|
+
estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
|
|
125
|
+
estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
|
|
126
|
+
} & {
|
|
127
|
+
readonly blockType: "staticBlocks" | "dynamicBlocks";
|
|
128
|
+
readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
129
|
+
} & {
|
|
130
|
+
readonly renderDelay: number;
|
|
131
|
+
readonly TooltipComponent: import("react").FC<any>;
|
|
132
|
+
readonly selectedFeatureId: string | undefined;
|
|
133
|
+
readonly DisplayMessageComponent: import("react").FC<any> | undefined;
|
|
134
|
+
} & {
|
|
135
|
+
readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
|
|
136
|
+
readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
|
|
137
|
+
getFeatureOverlapping(blockKey: string, x: number, y: number): any;
|
|
138
|
+
getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
|
|
139
|
+
searchFeatureByID(id: string): [number, number, number, number] | undefined;
|
|
140
|
+
readonly currentBytesRequested: number;
|
|
141
|
+
readonly currentFeatureScreenDensity: number;
|
|
142
|
+
readonly maxFeatureScreenDensity: any;
|
|
143
|
+
readonly estimatedStatsReady: boolean;
|
|
144
|
+
readonly maxAllowableBytes: number;
|
|
145
|
+
} & {
|
|
146
|
+
setMessage(message: string): void;
|
|
147
|
+
afterAttach(): void;
|
|
148
|
+
estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
|
|
149
|
+
headers?: Record<string, string> | undefined;
|
|
150
|
+
signal?: AbortSignal | undefined;
|
|
151
|
+
filters?: string[] | undefined;
|
|
152
|
+
}): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
|
|
153
|
+
setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
|
|
154
|
+
setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
|
|
155
|
+
clearRegionStats(): void;
|
|
156
|
+
setHeight(displayHeight: number): number;
|
|
157
|
+
resizeHeight(distance: number): number;
|
|
158
|
+
setScrollTop(scrollTop: number): void;
|
|
159
|
+
updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
|
|
160
|
+
addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
|
|
161
|
+
setCurrBpPerPx(n: number): void;
|
|
162
|
+
deleteBlock(key: string): void;
|
|
163
|
+
selectFeature(feature: import("@jbrowse/core/util").Feature): void;
|
|
164
|
+
clearFeatureSelection(): void;
|
|
165
|
+
setFeatureIdUnderMouse(feature: string | undefined): void;
|
|
166
|
+
reload(): void;
|
|
167
|
+
setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
|
|
168
|
+
} & {
|
|
169
|
+
readonly regionTooLarge: boolean;
|
|
170
|
+
readonly regionTooLargeReason: string;
|
|
171
|
+
} & {
|
|
172
|
+
reload(): Promise<void>;
|
|
173
|
+
afterAttach(): void;
|
|
174
|
+
} & {
|
|
175
|
+
regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
|
|
176
|
+
regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
|
|
177
|
+
trackMenuItems(): MenuItem[];
|
|
178
|
+
contextMenuItems(): {
|
|
179
|
+
label: string;
|
|
180
|
+
icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
|
|
181
|
+
onClick: () => void;
|
|
182
|
+
}[];
|
|
183
|
+
renderProps(): any;
|
|
184
|
+
} & {
|
|
185
|
+
renderSvg(opts: import("../LinearGenomeView").ExportSvgOptions & {
|
|
186
|
+
overrideHeight: number;
|
|
187
|
+
}): Promise<JSX.Element>;
|
|
188
|
+
} & {
|
|
189
|
+
readonly rendererTypeName: any;
|
|
190
|
+
readonly showLabels: any;
|
|
191
|
+
readonly showDescriptions: any;
|
|
192
|
+
readonly maxHeight: any;
|
|
193
|
+
readonly displayMode: any;
|
|
194
|
+
readonly rendererConfig: any;
|
|
195
|
+
} & {
|
|
196
|
+
toggleShowLabels(): void;
|
|
197
|
+
toggleShowDescriptions(): void;
|
|
198
|
+
setDisplayMode(val: string): void;
|
|
199
|
+
setMaxHeight(val: number): void;
|
|
200
|
+
} & {
|
|
201
|
+
renderProps(): any;
|
|
202
|
+
trackMenuItems(): MenuItem[];
|
|
203
|
+
}, import("mobx-state-tree")._NotCustomized, {
|
|
204
|
+
id: string;
|
|
205
|
+
type: string;
|
|
206
|
+
rpcDriverName: string | undefined;
|
|
207
|
+
height: number;
|
|
208
|
+
userBpPerPxLimit: number | undefined;
|
|
209
|
+
userByteSizeLimit: number | undefined;
|
|
210
|
+
} & import("mobx-state-tree")._NotCustomized>;
|
|
211
|
+
export declare type FeatureTrackStateModel = ReturnType<typeof stateModelFactory>;
|
|
212
|
+
export declare type FeatureTrackModel = Instance<FeatureTrackStateModel>;
|
|
213
|
+
export default stateModelFactory;
|
|
@@ -0,0 +1,162 @@
|
|
|
1
|
+
"use strict";
|
|
2
|
+
|
|
3
|
+
var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
|
|
4
|
+
|
|
5
|
+
Object.defineProperty(exports, "__esModule", {
|
|
6
|
+
value: true
|
|
7
|
+
});
|
|
8
|
+
exports["default"] = void 0;
|
|
9
|
+
|
|
10
|
+
var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
|
|
11
|
+
|
|
12
|
+
var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
|
|
13
|
+
|
|
14
|
+
var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
|
|
15
|
+
|
|
16
|
+
var _react = require("react");
|
|
17
|
+
|
|
18
|
+
var _configuration = require("@jbrowse/core/configuration");
|
|
19
|
+
|
|
20
|
+
var _util = require("@jbrowse/core/util");
|
|
21
|
+
|
|
22
|
+
var _mobxStateTree = require("mobx-state-tree");
|
|
23
|
+
|
|
24
|
+
var _Visibility = _interopRequireDefault(require("@material-ui/icons/Visibility"));
|
|
25
|
+
|
|
26
|
+
var _BaseLinearDisplay = require("../BaseLinearDisplay");
|
|
27
|
+
|
|
28
|
+
function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
|
|
29
|
+
|
|
30
|
+
function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
|
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31
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+
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32
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+
function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
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33
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+
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34
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+
function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2["default"])(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
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35
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+
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36
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+
var SetMaxHeightDlg = /*#__PURE__*/(0, _react.lazy)(function () {
|
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37
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+
return Promise.resolve().then(function () {
|
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38
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+
return _interopRequireWildcard(require('./components/SetMaxHeight'));
|
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39
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+
});
|
|
40
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+
});
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41
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+
|
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42
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+
var stateModelFactory = function stateModelFactory(configSchema) {
|
|
43
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+
return _mobxStateTree.types.compose('LinearBasicDisplay', _BaseLinearDisplay.BaseLinearDisplay, _mobxStateTree.types.model({
|
|
44
|
+
type: _mobxStateTree.types.literal('LinearBasicDisplay'),
|
|
45
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+
trackShowLabels: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
|
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46
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+
trackShowDescriptions: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
|
|
47
|
+
trackDisplayMode: _mobxStateTree.types.maybe(_mobxStateTree.types.string),
|
|
48
|
+
trackMaxHeight: _mobxStateTree.types.maybe(_mobxStateTree.types.number),
|
|
49
|
+
configuration: (0, _configuration.ConfigurationReference)(configSchema)
|
|
50
|
+
})).views(function (self) {
|
|
51
|
+
return {
|
|
52
|
+
get rendererTypeName() {
|
|
53
|
+
return (0, _configuration.getConf)(self, ['renderer', 'type']);
|
|
54
|
+
},
|
|
55
|
+
|
|
56
|
+
get showLabels() {
|
|
57
|
+
var _self$trackShowLabels;
|
|
58
|
+
|
|
59
|
+
return (_self$trackShowLabels = self.trackShowLabels) !== null && _self$trackShowLabels !== void 0 ? _self$trackShowLabels : (0, _configuration.getConf)(self, ['renderer', 'showLabels']);
|
|
60
|
+
},
|
|
61
|
+
|
|
62
|
+
get showDescriptions() {
|
|
63
|
+
var _self$trackShowDescri;
|
|
64
|
+
|
|
65
|
+
return (_self$trackShowDescri = self.trackShowDescriptions) !== null && _self$trackShowDescri !== void 0 ? _self$trackShowDescri : (0, _configuration.getConf)(self, ['renderer', 'showLabels']);
|
|
66
|
+
},
|
|
67
|
+
|
|
68
|
+
get maxHeight() {
|
|
69
|
+
var _self$trackMaxHeight;
|
|
70
|
+
|
|
71
|
+
return (_self$trackMaxHeight = self.trackMaxHeight) !== null && _self$trackMaxHeight !== void 0 ? _self$trackMaxHeight : (0, _configuration.getConf)(self, ['renderer', 'maxHeight']);
|
|
72
|
+
},
|
|
73
|
+
|
|
74
|
+
get displayMode() {
|
|
75
|
+
var _self$trackDisplayMod;
|
|
76
|
+
|
|
77
|
+
var displayMode = (0, _configuration.getConf)(self, ['renderer', 'displayMode']);
|
|
78
|
+
return (_self$trackDisplayMod = self.trackDisplayMode) !== null && _self$trackDisplayMod !== void 0 ? _self$trackDisplayMod : displayMode;
|
|
79
|
+
},
|
|
80
|
+
|
|
81
|
+
get rendererConfig() {
|
|
82
|
+
var configBlob = (0, _configuration.getConf)(self, ['renderer']) || {};
|
|
83
|
+
return self.rendererType.configSchema.create(_objectSpread(_objectSpread({}, configBlob), {}, {
|
|
84
|
+
showLabels: this.showLabels,
|
|
85
|
+
showDescriptions: this.showDescriptions,
|
|
86
|
+
displayMode: this.displayMode,
|
|
87
|
+
maxHeight: this.maxHeight
|
|
88
|
+
}), (0, _mobxStateTree.getEnv)(self));
|
|
89
|
+
}
|
|
90
|
+
|
|
91
|
+
};
|
|
92
|
+
}).actions(function (self) {
|
|
93
|
+
return {
|
|
94
|
+
toggleShowLabels: function toggleShowLabels() {
|
|
95
|
+
self.trackShowLabels = !self.showLabels;
|
|
96
|
+
},
|
|
97
|
+
toggleShowDescriptions: function toggleShowDescriptions() {
|
|
98
|
+
self.trackShowDescriptions = !self.showDescriptions;
|
|
99
|
+
},
|
|
100
|
+
setDisplayMode: function setDisplayMode(val) {
|
|
101
|
+
self.trackDisplayMode = val;
|
|
102
|
+
},
|
|
103
|
+
setMaxHeight: function setMaxHeight(val) {
|
|
104
|
+
self.trackMaxHeight = val;
|
|
105
|
+
}
|
|
106
|
+
};
|
|
107
|
+
}).views(function (self) {
|
|
108
|
+
var superTrackMenuItems = self.trackMenuItems,
|
|
109
|
+
superRenderProps = self.renderProps;
|
|
110
|
+
return {
|
|
111
|
+
renderProps: function renderProps() {
|
|
112
|
+
var config = self.rendererConfig;
|
|
113
|
+
return _objectSpread(_objectSpread({}, superRenderProps()), {}, {
|
|
114
|
+
config: config
|
|
115
|
+
});
|
|
116
|
+
},
|
|
117
|
+
trackMenuItems: function trackMenuItems() {
|
|
118
|
+
return [].concat((0, _toConsumableArray2["default"])(superTrackMenuItems()), [{
|
|
119
|
+
label: 'Show labels',
|
|
120
|
+
icon: _Visibility["default"],
|
|
121
|
+
type: 'checkbox',
|
|
122
|
+
checked: self.showLabels,
|
|
123
|
+
onClick: function onClick() {
|
|
124
|
+
self.toggleShowLabels();
|
|
125
|
+
}
|
|
126
|
+
}, {
|
|
127
|
+
label: 'Show descriptions',
|
|
128
|
+
icon: _Visibility["default"],
|
|
129
|
+
type: 'checkbox',
|
|
130
|
+
checked: self.showDescriptions,
|
|
131
|
+
onClick: function onClick() {
|
|
132
|
+
self.toggleShowDescriptions();
|
|
133
|
+
}
|
|
134
|
+
}, {
|
|
135
|
+
label: 'Display mode',
|
|
136
|
+
icon: _Visibility["default"],
|
|
137
|
+
subMenu: ['compact', 'reducedRepresentation', 'normal', 'collapse'].map(function (val) {
|
|
138
|
+
return {
|
|
139
|
+
label: val,
|
|
140
|
+
onClick: function onClick() {
|
|
141
|
+
self.setDisplayMode(val);
|
|
142
|
+
}
|
|
143
|
+
};
|
|
144
|
+
})
|
|
145
|
+
}, {
|
|
146
|
+
label: 'Set max height',
|
|
147
|
+
onClick: function onClick() {
|
|
148
|
+
(0, _util.getSession)(self).queueDialog(function (doneCallback) {
|
|
149
|
+
return [SetMaxHeightDlg, {
|
|
150
|
+
model: self,
|
|
151
|
+
handleClose: doneCallback
|
|
152
|
+
}];
|
|
153
|
+
});
|
|
154
|
+
}
|
|
155
|
+
}]);
|
|
156
|
+
}
|
|
157
|
+
};
|
|
158
|
+
});
|
|
159
|
+
};
|
|
160
|
+
|
|
161
|
+
var _default = stateModelFactory;
|
|
162
|
+
exports["default"] = _default;
|
|
@@ -1,14 +1,14 @@
|
|
|
1
|
-
/// <reference types="react" />
|
|
2
|
-
import { Instance } from 'mobx-state-tree';
|
|
3
|
-
import { LinearGenomeViewStateModel } from '..';
|
|
4
|
-
declare type LGV = Instance<LinearGenomeViewStateModel>;
|
|
5
|
-
declare function CenterLine({ model }: {
|
|
6
|
-
model: LGV;
|
|
7
|
-
}): JSX.Element | null;
|
|
8
|
-
declare namespace CenterLine {
|
|
9
|
-
var propTypes: {
|
|
10
|
-
model: import("prop-types").Validator<any>;
|
|
11
|
-
};
|
|
12
|
-
}
|
|
13
|
-
declare const _default: typeof CenterLine;
|
|
14
|
-
export default _default;
|
|
1
|
+
/// <reference types="react" />
|
|
2
|
+
import { Instance } from 'mobx-state-tree';
|
|
3
|
+
import { LinearGenomeViewStateModel } from '..';
|
|
4
|
+
declare type LGV = Instance<LinearGenomeViewStateModel>;
|
|
5
|
+
declare function CenterLine({ model }: {
|
|
6
|
+
model: LGV;
|
|
7
|
+
}): JSX.Element | null;
|
|
8
|
+
declare namespace CenterLine {
|
|
9
|
+
var propTypes: {
|
|
10
|
+
model: import("prop-types").Validator<any>;
|
|
11
|
+
};
|
|
12
|
+
}
|
|
13
|
+
declare const _default: typeof CenterLine;
|
|
14
|
+
export default _default;
|