@jbrowse/plugin-linear-comparative-view 2.12.0 → 2.12.1
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/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js +1 -1
- package/dist/LGVSyntenyDisplay/components/util.js +1 -2
- package/dist/LGVSyntenyDisplay/index.js +1 -1
- package/dist/LGVSyntenyDisplay/model.d.ts +35 -36
- package/dist/LaunchLinearSyntenyView.js +1 -1
- package/dist/LinearComparativeDisplay/index.js +1 -1
- package/dist/LinearComparativeDisplay/stateModelFactory.d.ts +34 -49
- package/dist/LinearComparativeView/index.js +1 -1
- package/dist/LinearComparativeView/model.d.ts +21 -150
- package/dist/LinearReadVsRef/LinearReadVsRef.js +1 -1
- package/dist/LinearReadVsRef/index.js +1 -1
- package/dist/LinearSyntenyDisplay/afterAttach.js +1 -2
- package/dist/LinearSyntenyDisplay/components/SyntenyContextMenu.js +1 -1
- package/dist/LinearSyntenyDisplay/components/util.js +7 -8
- package/dist/LinearSyntenyDisplay/drawSynteny.js +4 -4
- package/dist/LinearSyntenyDisplay/index.js +1 -1
- package/dist/LinearSyntenyDisplay/model.d.ts +26 -36
- package/dist/LinearSyntenyView/components/ExportSvgDialog.js +1 -1
- package/dist/LinearSyntenyView/components/Icons.js +2 -3
- package/dist/LinearSyntenyView/components/ImportForm/util.js +4 -5
- package/dist/LinearSyntenyView/index.js +1 -1
- package/dist/LinearSyntenyView/model.d.ts +24 -838
- package/dist/LinearSyntenyView/model.js +1 -1
- package/dist/LinearSyntenyView/svgcomponents/SVGBackground.js +1 -1
- package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js +1 -2
- package/dist/SyntenyFeatureDetail/index.js +1 -1
- package/dist/SyntenyTrack/index.js +1 -1
- package/dist/util.js +5 -6
- package/esm/LGVSyntenyDisplay/model.d.ts +35 -36
- package/esm/LinearComparativeDisplay/stateModelFactory.d.ts +34 -49
- package/esm/LinearComparativeView/model.d.ts +21 -150
- package/esm/LinearSyntenyDisplay/model.d.ts +26 -36
- package/esm/LinearSyntenyView/model.d.ts +24 -838
- package/package.json +2 -2
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@@ -67,15 +67,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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} & {
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volatileWidth: number | undefined;
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minimumBlockWidth: number;
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draggingTrackId:
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draggingTrackId: undefined | string;
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volatileError: unknown;
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afterDisplayedRegionsSetCallbacks: Function[];
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scaleFactor: number;
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trackRefs: Record<string, HTMLDivElement>;
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coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
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coarseTotalBp: number;
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leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
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rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
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} & {
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readonly trackLabelsSetting: any;
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readonly width: number;
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@@ -124,8 +124,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
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scrollTo(offsetPx: number): number;
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zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
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setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string
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setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
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setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
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setNewView(bpPerPx: number, offsetPx: number): void;
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horizontallyFlip(): void;
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showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
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moveTrack(movingId: string, targetId: string): void;
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closeView(): void;
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toggleTrack(trackId: string): boolean;
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setTrackLabels(setting: "
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setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
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setShowCenterLine(b: boolean): void;
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setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
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activateTrackSelector(): import("@jbrowse/core/util").Widget;
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getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
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start: number;
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end: number;
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type: string;
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regionNumber?: number
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reversed?: boolean
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regionNumber?: number;
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reversed?: boolean;
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refName: string;
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assemblyName: string;
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key: string;
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offsetPx: number;
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widthPx: number;
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variant?: string
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isLeftEndOfDisplayedRegion?: boolean
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variant?: string;
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isLeftEndOfDisplayedRegion?: boolean;
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}[];
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afterDisplayedRegionsSet(cb: Function): void;
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horizontalScroll(distance: number): number;
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center(): void;
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showAllRegions(): void;
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showAllRegionsInAssembly(assemblyName?: string
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setDraggingTrackId(idx?: string
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showAllRegionsInAssembly(assemblyName?: string): void;
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setDraggingTrackId(idx?: string): void;
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setScaleFactor(factor: number): void;
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clearView(): void;
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exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
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@@ -186,141 +186,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
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afterAttach(): void;
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} & {
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moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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navToLocString(input: string, optAssemblyName?: string
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moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
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navToLocString(input: string, optAssemblyName?: string): Promise<void>;
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navToSearchString({ input, assembly, }: {
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input: string;
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assembly:
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configuration: any;
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} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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loaded: boolean;
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loadingP: Promise<void> | undefined;
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volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: {
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lowerCaseRefNameAliases: {
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} | undefined; /**
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* #property
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*/
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cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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getConf(arg: string): any;
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} & {
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readonly initialized: boolean;
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readonly name: string;
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readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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readonly aliases: string[];
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readonly displayName: string | undefined;
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hasName(name: string): boolean;
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readonly allAliases: string[];
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readonly allRefNames: string[] | undefined;
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readonly lowerCaseRefNames: string[] | undefined;
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readonly allRefNamesWithLowerCase: string[] | undefined;
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readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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readonly refNameColors: string[];
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readonly refNames: string[] | undefined;
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getCanonicalRefName(refName: string): string | undefined;
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getRefNameColor(refName: string): string | undefined;
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setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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setError(e: unknown): void;
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setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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setLoadingP(p?: Promise<void> | undefined): void;
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load(): Promise<void>;
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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}>;
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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}, {
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volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: {
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} | undefined; /**
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*/
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} & {
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readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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readonly aliases: string[];
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readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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readonly refNameColors: string[];
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readonly refNames: string[] | undefined;
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} & {
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getCanonicalRefName(refName: string): string | undefined;
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getRefNameColor(refName: string): string | undefined;
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} & {
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setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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setError(e: unknown): void;
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setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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}, lcAliases: {
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}): void;
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setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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setLoadingP(p?: Promise<void> | undefined): void;
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load(): Promise<void>;
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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}>;
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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}>;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
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}): Promise<void>;
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navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
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navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
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} & {
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bpToPx({ refName, coord, regionNumber, }: {
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centerAt(coord: number, refName: string, regionNumber?: number): void;
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};
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coord: number;
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} | undefined;
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} & {
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afterCreate(): void;
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} & {
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onSubviewAction(actionName: string, path: string, args?: unknown[]
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+
onSubviewAction(actionName: string, path: string, args?: unknown[]): void;
|
|
406
278
|
setWidth(newWidth: number): void;
|
|
407
|
-
setViews(views: import("mobx-state-tree").
|
|
408
|
-
|
|
409
|
-
displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
410
|
-
minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
411
|
-
} & {
|
|
412
|
-
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
413
|
-
type: import("mobx-state-tree").IType<string | undefined, string, string>;
|
|
414
|
-
offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
415
|
-
bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
416
|
-
displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
|
|
417
|
-
tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
|
|
418
|
-
hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
419
|
-
hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
420
|
-
hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
421
|
-
trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
422
|
-
showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
423
|
-
showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
424
|
-
trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
425
|
-
showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
426
|
-
highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
|
|
427
|
-
colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
428
|
-
}>>[]): void;
|
|
429
|
-
removeView(view: {
|
|
430
|
-
id: string;
|
|
431
|
-
displayName: string | undefined;
|
|
432
|
-
minimized: boolean;
|
|
433
|
-
type: string;
|
|
434
|
-
offsetPx: number;
|
|
435
|
-
bpPerPx: number;
|
|
436
|
-
displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
|
|
437
|
-
tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
|
|
438
|
-
hideHeader: boolean;
|
|
439
|
-
hideHeaderOverview: boolean;
|
|
440
|
-
hideNoTracksActive: boolean;
|
|
441
|
-
trackSelectorType: string;
|
|
442
|
-
showCenterLine: boolean;
|
|
443
|
-
showCytobandsSetting: boolean;
|
|
444
|
-
trackLabels: string;
|
|
445
|
-
showGridlines: boolean;
|
|
446
|
-
highlight: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>>;
|
|
447
|
-
colorByCDS: boolean;
|
|
448
|
-
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
|
449
|
-
width: number;
|
|
450
|
-
} & {
|
|
451
|
-
menuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
452
|
-
} & {
|
|
453
|
-
setDisplayName(name: string): void;
|
|
454
|
-
setWidth(newWidth: number): void;
|
|
455
|
-
setMinimized(flag: boolean): void;
|
|
456
|
-
} & {
|
|
457
|
-
volatileWidth: number | undefined;
|
|
458
|
-
minimumBlockWidth: number;
|
|
459
|
-
draggingTrackId: string | undefined;
|
|
460
|
-
volatileError: unknown;
|
|
461
|
-
afterDisplayedRegionsSetCallbacks: Function[];
|
|
462
|
-
scaleFactor: number;
|
|
463
|
-
trackRefs: Record<string, HTMLDivElement>;
|
|
464
|
-
coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
|
|
465
|
-
coarseTotalBp: number;
|
|
466
|
-
leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
|
|
467
|
-
rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
|
|
468
|
-
} & {
|
|
469
|
-
readonly trackLabelsSetting: any;
|
|
470
|
-
readonly width: number;
|
|
471
|
-
readonly interRegionPaddingWidth: number;
|
|
472
|
-
readonly assemblyNames: string[];
|
|
473
|
-
} & {
|
|
474
|
-
MiniControlsComponent(): React.FC<any>;
|
|
475
|
-
HeaderComponent(): React.FC<any>;
|
|
476
|
-
readonly assemblyErrors: string;
|
|
477
|
-
readonly assembliesInitialized: boolean;
|
|
478
|
-
readonly initialized: boolean;
|
|
479
|
-
readonly hasDisplayedRegions: boolean;
|
|
480
|
-
readonly scaleBarHeight: number;
|
|
481
|
-
readonly headerHeight: number;
|
|
482
|
-
readonly trackHeights: number;
|
|
483
|
-
readonly trackHeightsWithResizeHandles: number;
|
|
484
|
-
readonly height: number;
|
|
485
|
-
readonly totalBp: number;
|
|
486
|
-
readonly maxBpPerPx: number;
|
|
487
|
-
readonly minBpPerPx: number;
|
|
488
|
-
readonly error: {};
|
|
489
|
-
readonly maxOffset: number;
|
|
490
|
-
readonly minOffset: number;
|
|
491
|
-
readonly displayedRegionsTotalPx: number;
|
|
492
|
-
renderProps(): any;
|
|
493
|
-
searchScope(assemblyName: string): {
|
|
494
|
-
assemblyName: string;
|
|
495
|
-
includeAggregateIndexes: boolean;
|
|
496
|
-
tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
|
|
497
|
-
};
|
|
498
|
-
getTrack(id: string): any;
|
|
499
|
-
rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
|
|
500
|
-
rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
|
|
501
|
-
readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
|
|
502
|
-
} & {
|
|
503
|
-
setColorByCDS(flag: boolean): void;
|
|
504
|
-
setShowCytobands(flag: boolean): void;
|
|
505
|
-
setWidth(newWidth: number): void;
|
|
506
|
-
setError(error: unknown): void;
|
|
507
|
-
setHideHeader(b: boolean): void;
|
|
508
|
-
setHideHeaderOverview(b: boolean): void;
|
|
509
|
-
setHideNoTracksActive(b: boolean): void;
|
|
510
|
-
setShowGridlines(b: boolean): void;
|
|
511
|
-
addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
|
|
512
|
-
setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
|
|
513
|
-
removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
|
|
514
|
-
scrollTo(offsetPx: number): number;
|
|
515
|
-
zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
|
|
516
|
-
setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
|
|
517
|
-
setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
|
|
518
|
-
setNewView(bpPerPx: number, offsetPx: number): void;
|
|
519
|
-
horizontallyFlip(): void;
|
|
520
|
-
showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
|
|
521
|
-
hideTrack(trackId: string): number;
|
|
522
|
-
} & {
|
|
523
|
-
moveTrackDown(id: string): void;
|
|
524
|
-
moveTrackUp(id: string): void;
|
|
525
|
-
moveTrackToTop(id: string): void;
|
|
526
|
-
moveTrackToBottom(id: string): void;
|
|
527
|
-
moveTrack(movingId: string, targetId: string): void;
|
|
528
|
-
closeView(): void;
|
|
529
|
-
toggleTrack(trackId: string): boolean;
|
|
530
|
-
setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
|
|
531
|
-
setShowCenterLine(b: boolean): void;
|
|
532
|
-
setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
|
|
533
|
-
activateTrackSelector(): import("@jbrowse/core/util").Widget;
|
|
534
|
-
getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
|
|
535
|
-
start: number;
|
|
536
|
-
end: number;
|
|
537
|
-
type: string;
|
|
538
|
-
regionNumber?: number | undefined;
|
|
539
|
-
reversed?: boolean | undefined;
|
|
540
|
-
refName: string;
|
|
541
|
-
assemblyName: string;
|
|
542
|
-
key: string;
|
|
543
|
-
offsetPx: number;
|
|
544
|
-
widthPx: number;
|
|
545
|
-
variant?: string | undefined;
|
|
546
|
-
isLeftEndOfDisplayedRegion?: boolean | undefined;
|
|
547
|
-
}[];
|
|
548
|
-
afterDisplayedRegionsSet(cb: Function): void;
|
|
549
|
-
horizontalScroll(distance: number): number;
|
|
550
|
-
center(): void;
|
|
551
|
-
showAllRegions(): void;
|
|
552
|
-
showAllRegionsInAssembly(assemblyName?: string | undefined): void;
|
|
553
|
-
setDraggingTrackId(idx?: string | undefined): void;
|
|
554
|
-
setScaleFactor(factor: number): void;
|
|
555
|
-
clearView(): void;
|
|
556
|
-
exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
|
|
557
|
-
} & {
|
|
558
|
-
slide: (viewWidths: number) => void;
|
|
559
|
-
} & {
|
|
560
|
-
zoom: (targetBpPerPx: number) => void;
|
|
561
|
-
} & {
|
|
562
|
-
readonly canShowCytobands: boolean;
|
|
563
|
-
readonly showCytobands: boolean;
|
|
564
|
-
readonly anyCytobandsExist: boolean;
|
|
565
|
-
readonly cytobandOffset: number;
|
|
566
|
-
} & {
|
|
567
|
-
menuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
568
|
-
} & {
|
|
569
|
-
readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
570
|
-
readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
571
|
-
readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
|
|
572
|
-
readonly visibleLocStrings: string;
|
|
573
|
-
readonly coarseVisibleLocStrings: string;
|
|
574
|
-
} & {
|
|
575
|
-
setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
|
|
576
|
-
afterAttach(): void;
|
|
577
|
-
} & {
|
|
578
|
-
moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
|
|
579
|
-
navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
|
|
580
|
-
navToSearchString({ input, assembly, }: {
|
|
581
|
-
input: string;
|
|
582
|
-
assembly: {
|
|
583
|
-
configuration: any;
|
|
584
|
-
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
|
585
|
-
error: unknown;
|
|
586
|
-
loaded: boolean;
|
|
587
|
-
loadingP: Promise<void> | undefined;
|
|
588
|
-
volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
589
|
-
refNameAliases: {
|
|
590
|
-
[x: string]: string | undefined;
|
|
591
|
-
} | undefined;
|
|
592
|
-
lowerCaseRefNameAliases: {
|
|
593
|
-
[x: string]: string | undefined;
|
|
594
|
-
} | undefined; /**
|
|
595
|
-
* #property
|
|
596
|
-
*/
|
|
597
|
-
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
598
|
-
} & {
|
|
599
|
-
getConf(arg: string): any;
|
|
600
|
-
} & {
|
|
601
|
-
readonly initialized: boolean;
|
|
602
|
-
readonly name: string;
|
|
603
|
-
readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
604
|
-
readonly aliases: string[];
|
|
605
|
-
readonly displayName: string | undefined;
|
|
606
|
-
hasName(name: string): boolean;
|
|
607
|
-
readonly allAliases: string[];
|
|
608
|
-
readonly allRefNames: string[] | undefined;
|
|
609
|
-
readonly lowerCaseRefNames: string[] | undefined;
|
|
610
|
-
readonly allRefNamesWithLowerCase: string[] | undefined;
|
|
611
|
-
readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
|
|
612
|
-
readonly refNameColors: string[];
|
|
613
|
-
} & {
|
|
614
|
-
readonly refNames: string[] | undefined;
|
|
615
|
-
} & {
|
|
616
|
-
getCanonicalRefName(refName: string): string | undefined;
|
|
617
|
-
getRefNameColor(refName: string): string | undefined;
|
|
618
|
-
isValidRefName(refName: string): boolean;
|
|
619
|
-
} & {
|
|
620
|
-
setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
|
|
621
|
-
setError(e: unknown): void;
|
|
622
|
-
setRegions(regions: import("@jbrowse/core/util").Region[]): void;
|
|
623
|
-
setRefNameAliases(aliases: {
|
|
624
|
-
[x: string]: string | undefined;
|
|
625
|
-
}, lcAliases: {
|
|
626
|
-
[x: string]: string | undefined;
|
|
627
|
-
}): void;
|
|
628
|
-
setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
|
|
629
|
-
setLoadingP(p?: Promise<void> | undefined): void;
|
|
630
|
-
load(): Promise<void>;
|
|
631
|
-
loadPre(): Promise<void>;
|
|
632
|
-
} & {
|
|
633
|
-
getAdapterMapEntry(adapterConf: {
|
|
634
|
-
[x: string]: unknown;
|
|
635
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
|
|
636
|
-
getRefNameMapForAdapter(adapterConf: {
|
|
637
|
-
[x: string]: unknown;
|
|
638
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
639
|
-
[x: string]: string | undefined;
|
|
640
|
-
}>;
|
|
641
|
-
getReverseRefNameMapForAdapter(adapterConf: {
|
|
642
|
-
[x: string]: unknown;
|
|
643
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
644
|
-
[x: string]: string | undefined;
|
|
645
|
-
}>;
|
|
646
|
-
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
647
|
-
configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
|
|
648
|
-
}, {
|
|
649
|
-
error: unknown;
|
|
650
|
-
loaded: boolean;
|
|
651
|
-
loadingP: Promise<void> | undefined;
|
|
652
|
-
volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
653
|
-
refNameAliases: {
|
|
654
|
-
[x: string]: string | undefined;
|
|
655
|
-
} | undefined;
|
|
656
|
-
lowerCaseRefNameAliases: {
|
|
657
|
-
[x: string]: string | undefined;
|
|
658
|
-
} | undefined; /**
|
|
659
|
-
* #property
|
|
660
|
-
*/
|
|
661
|
-
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
662
|
-
} & {
|
|
663
|
-
getConf(arg: string): any;
|
|
664
|
-
} & {
|
|
665
|
-
readonly initialized: boolean;
|
|
666
|
-
readonly name: string;
|
|
667
|
-
readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
668
|
-
readonly aliases: string[];
|
|
669
|
-
readonly displayName: string | undefined;
|
|
670
|
-
hasName(name: string): boolean;
|
|
671
|
-
readonly allAliases: string[];
|
|
672
|
-
readonly allRefNames: string[] | undefined;
|
|
673
|
-
readonly lowerCaseRefNames: string[] | undefined;
|
|
674
|
-
readonly allRefNamesWithLowerCase: string[] | undefined;
|
|
675
|
-
readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
|
|
676
|
-
readonly refNameColors: string[];
|
|
677
|
-
} & {
|
|
678
|
-
readonly refNames: string[] | undefined;
|
|
679
|
-
} & {
|
|
680
|
-
getCanonicalRefName(refName: string): string | undefined;
|
|
681
|
-
getRefNameColor(refName: string): string | undefined;
|
|
682
|
-
isValidRefName(refName: string): boolean;
|
|
683
|
-
} & {
|
|
684
|
-
setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
|
|
685
|
-
setError(e: unknown): void;
|
|
686
|
-
setRegions(regions: import("@jbrowse/core/util").Region[]): void;
|
|
687
|
-
setRefNameAliases(aliases: {
|
|
688
|
-
[x: string]: string | undefined;
|
|
689
|
-
}, lcAliases: {
|
|
690
|
-
[x: string]: string | undefined;
|
|
691
|
-
}): void;
|
|
692
|
-
setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
|
|
693
|
-
setLoadingP(p?: Promise<void> | undefined): void;
|
|
694
|
-
load(): Promise<void>;
|
|
695
|
-
loadPre(): Promise<void>;
|
|
696
|
-
} & {
|
|
697
|
-
getAdapterMapEntry(adapterConf: {
|
|
698
|
-
[x: string]: unknown;
|
|
699
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
|
|
700
|
-
getRefNameMapForAdapter(adapterConf: {
|
|
701
|
-
[x: string]: unknown;
|
|
702
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
703
|
-
[x: string]: string | undefined;
|
|
704
|
-
}>;
|
|
705
|
-
getReverseRefNameMapForAdapter(adapterConf: {
|
|
706
|
-
[x: string]: unknown;
|
|
707
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
708
|
-
[x: string]: string | undefined;
|
|
709
|
-
}>;
|
|
710
|
-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
711
|
-
}): Promise<void>;
|
|
712
|
-
navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
|
|
713
|
-
navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
|
|
714
|
-
navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
|
|
715
|
-
} & {
|
|
716
|
-
rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
717
|
-
bpToPx({ refName, coord, regionNumber, }: {
|
|
718
|
-
refName: string;
|
|
719
|
-
coord: number;
|
|
720
|
-
regionNumber?: number | undefined;
|
|
721
|
-
}): {
|
|
722
|
-
index: number;
|
|
723
|
-
offsetPx: number;
|
|
724
|
-
} | undefined;
|
|
725
|
-
centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
|
|
726
|
-
pxToBp(px: number): {
|
|
727
|
-
coord: number;
|
|
728
|
-
index: number;
|
|
729
|
-
refName: string;
|
|
730
|
-
oob: boolean;
|
|
731
|
-
assemblyName: string;
|
|
732
|
-
offset: number;
|
|
733
|
-
start: number;
|
|
734
|
-
end: number;
|
|
735
|
-
reversed?: boolean | undefined;
|
|
736
|
-
};
|
|
737
|
-
readonly centerLineInfo: {
|
|
738
|
-
coord: number;
|
|
739
|
-
index: number;
|
|
740
|
-
refName: string;
|
|
741
|
-
oob: boolean;
|
|
742
|
-
assemblyName: string;
|
|
743
|
-
offset: number;
|
|
744
|
-
start: number;
|
|
745
|
-
end: number;
|
|
746
|
-
reversed?: boolean | undefined;
|
|
747
|
-
} | undefined;
|
|
748
|
-
} & {
|
|
749
|
-
afterCreate(): void;
|
|
750
|
-
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
751
|
-
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
752
|
-
displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
753
|
-
minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
754
|
-
} & {
|
|
755
|
-
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
756
|
-
type: import("mobx-state-tree").IType<string | undefined, string, string>;
|
|
757
|
-
offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
758
|
-
bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
759
|
-
displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
|
|
760
|
-
tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
|
|
761
|
-
hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
762
|
-
hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
763
|
-
hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
764
|
-
trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
765
|
-
showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
766
|
-
showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
767
|
-
trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
768
|
-
showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
769
|
-
highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
|
|
770
|
-
colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
771
|
-
}, {
|
|
772
|
-
width: number;
|
|
773
|
-
} & {
|
|
774
|
-
menuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
775
|
-
} & {
|
|
776
|
-
setDisplayName(name: string): void;
|
|
777
|
-
setWidth(newWidth: number): void;
|
|
778
|
-
setMinimized(flag: boolean): void;
|
|
779
|
-
} & {
|
|
780
|
-
volatileWidth: number | undefined;
|
|
781
|
-
minimumBlockWidth: number;
|
|
782
|
-
draggingTrackId: string | undefined;
|
|
783
|
-
volatileError: unknown;
|
|
784
|
-
afterDisplayedRegionsSetCallbacks: Function[];
|
|
785
|
-
scaleFactor: number;
|
|
786
|
-
trackRefs: Record<string, HTMLDivElement>;
|
|
787
|
-
coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
|
|
788
|
-
coarseTotalBp: number;
|
|
789
|
-
leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
|
|
790
|
-
rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
|
|
791
|
-
} & {
|
|
792
|
-
readonly trackLabelsSetting: any;
|
|
793
|
-
readonly width: number;
|
|
794
|
-
readonly interRegionPaddingWidth: number;
|
|
795
|
-
readonly assemblyNames: string[];
|
|
796
|
-
} & {
|
|
797
|
-
MiniControlsComponent(): React.FC<any>;
|
|
798
|
-
HeaderComponent(): React.FC<any>;
|
|
799
|
-
readonly assemblyErrors: string;
|
|
800
|
-
readonly assembliesInitialized: boolean;
|
|
801
|
-
readonly initialized: boolean;
|
|
802
|
-
readonly hasDisplayedRegions: boolean;
|
|
803
|
-
readonly scaleBarHeight: number;
|
|
804
|
-
readonly headerHeight: number;
|
|
805
|
-
readonly trackHeights: number;
|
|
806
|
-
readonly trackHeightsWithResizeHandles: number;
|
|
807
|
-
readonly height: number;
|
|
808
|
-
readonly totalBp: number;
|
|
809
|
-
readonly maxBpPerPx: number;
|
|
810
|
-
readonly minBpPerPx: number;
|
|
811
|
-
readonly error: {};
|
|
812
|
-
readonly maxOffset: number;
|
|
813
|
-
readonly minOffset: number;
|
|
814
|
-
readonly displayedRegionsTotalPx: number;
|
|
815
|
-
renderProps(): any;
|
|
816
|
-
searchScope(assemblyName: string): {
|
|
817
|
-
assemblyName: string;
|
|
818
|
-
includeAggregateIndexes: boolean;
|
|
819
|
-
tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
|
|
820
|
-
};
|
|
821
|
-
getTrack(id: string): any;
|
|
822
|
-
rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
|
|
823
|
-
rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
|
|
824
|
-
readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
|
|
825
|
-
} & {
|
|
826
|
-
setColorByCDS(flag: boolean): void;
|
|
827
|
-
setShowCytobands(flag: boolean): void;
|
|
828
|
-
setWidth(newWidth: number): void;
|
|
829
|
-
setError(error: unknown): void;
|
|
830
|
-
setHideHeader(b: boolean): void;
|
|
831
|
-
setHideHeaderOverview(b: boolean): void;
|
|
832
|
-
setHideNoTracksActive(b: boolean): void;
|
|
833
|
-
setShowGridlines(b: boolean): void;
|
|
834
|
-
addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
|
|
835
|
-
setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
|
|
836
|
-
removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
|
|
837
|
-
scrollTo(offsetPx: number): number;
|
|
838
|
-
zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
|
|
839
|
-
setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
|
|
840
|
-
setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
|
|
841
|
-
setNewView(bpPerPx: number, offsetPx: number): void;
|
|
842
|
-
horizontallyFlip(): void;
|
|
843
|
-
showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
|
|
844
|
-
hideTrack(trackId: string): number;
|
|
845
|
-
} & {
|
|
846
|
-
moveTrackDown(id: string): void;
|
|
847
|
-
moveTrackUp(id: string): void;
|
|
848
|
-
moveTrackToTop(id: string): void;
|
|
849
|
-
moveTrackToBottom(id: string): void;
|
|
850
|
-
moveTrack(movingId: string, targetId: string): void;
|
|
851
|
-
closeView(): void;
|
|
852
|
-
toggleTrack(trackId: string): boolean;
|
|
853
|
-
setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
|
|
854
|
-
setShowCenterLine(b: boolean): void;
|
|
855
|
-
setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
|
|
856
|
-
activateTrackSelector(): import("@jbrowse/core/util").Widget;
|
|
857
|
-
getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
|
|
858
|
-
start: number;
|
|
859
|
-
end: number;
|
|
860
|
-
type: string;
|
|
861
|
-
regionNumber?: number | undefined;
|
|
862
|
-
reversed?: boolean | undefined;
|
|
863
|
-
refName: string;
|
|
864
|
-
assemblyName: string;
|
|
865
|
-
key: string;
|
|
866
|
-
offsetPx: number;
|
|
867
|
-
widthPx: number;
|
|
868
|
-
variant?: string | undefined;
|
|
869
|
-
isLeftEndOfDisplayedRegion?: boolean | undefined;
|
|
870
|
-
}[];
|
|
871
|
-
afterDisplayedRegionsSet(cb: Function): void;
|
|
872
|
-
horizontalScroll(distance: number): number;
|
|
873
|
-
center(): void;
|
|
874
|
-
showAllRegions(): void;
|
|
875
|
-
showAllRegionsInAssembly(assemblyName?: string | undefined): void;
|
|
876
|
-
setDraggingTrackId(idx?: string | undefined): void;
|
|
877
|
-
setScaleFactor(factor: number): void;
|
|
878
|
-
clearView(): void;
|
|
879
|
-
exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
|
|
880
|
-
} & {
|
|
881
|
-
slide: (viewWidths: number) => void;
|
|
882
|
-
} & {
|
|
883
|
-
zoom: (targetBpPerPx: number) => void;
|
|
884
|
-
} & {
|
|
885
|
-
readonly canShowCytobands: boolean;
|
|
886
|
-
readonly showCytobands: boolean;
|
|
887
|
-
readonly anyCytobandsExist: boolean;
|
|
888
|
-
readonly cytobandOffset: number;
|
|
889
|
-
} & {
|
|
890
|
-
menuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
891
|
-
} & {
|
|
892
|
-
readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
893
|
-
readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
894
|
-
readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
|
|
895
|
-
readonly visibleLocStrings: string;
|
|
896
|
-
readonly coarseVisibleLocStrings: string;
|
|
897
|
-
} & {
|
|
898
|
-
setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
|
|
899
|
-
afterAttach(): void;
|
|
900
|
-
} & {
|
|
901
|
-
moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
|
|
902
|
-
navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
|
|
903
|
-
navToSearchString({ input, assembly, }: {
|
|
904
|
-
input: string;
|
|
905
|
-
assembly: {
|
|
906
|
-
configuration: any;
|
|
907
|
-
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
|
908
|
-
error: unknown;
|
|
909
|
-
loaded: boolean;
|
|
910
|
-
loadingP: Promise<void> | undefined;
|
|
911
|
-
volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
912
|
-
refNameAliases: {
|
|
913
|
-
[x: string]: string | undefined;
|
|
914
|
-
} | undefined;
|
|
915
|
-
lowerCaseRefNameAliases: {
|
|
916
|
-
[x: string]: string | undefined;
|
|
917
|
-
} | undefined; /**
|
|
918
|
-
* #property
|
|
919
|
-
*/
|
|
920
|
-
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
921
|
-
} & {
|
|
922
|
-
getConf(arg: string): any;
|
|
923
|
-
} & {
|
|
924
|
-
readonly initialized: boolean;
|
|
925
|
-
readonly name: string;
|
|
926
|
-
readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
927
|
-
readonly aliases: string[];
|
|
928
|
-
readonly displayName: string | undefined;
|
|
929
|
-
hasName(name: string): boolean;
|
|
930
|
-
readonly allAliases: string[];
|
|
931
|
-
readonly allRefNames: string[] | undefined;
|
|
932
|
-
readonly lowerCaseRefNames: string[] | undefined;
|
|
933
|
-
readonly allRefNamesWithLowerCase: string[] | undefined;
|
|
934
|
-
readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
|
|
935
|
-
readonly refNameColors: string[];
|
|
936
|
-
} & {
|
|
937
|
-
readonly refNames: string[] | undefined;
|
|
938
|
-
} & {
|
|
939
|
-
getCanonicalRefName(refName: string): string | undefined;
|
|
940
|
-
getRefNameColor(refName: string): string | undefined;
|
|
941
|
-
isValidRefName(refName: string): boolean;
|
|
942
|
-
} & {
|
|
943
|
-
setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
|
|
944
|
-
setError(e: unknown): void;
|
|
945
|
-
setRegions(regions: import("@jbrowse/core/util").Region[]): void;
|
|
946
|
-
setRefNameAliases(aliases: {
|
|
947
|
-
[x: string]: string | undefined;
|
|
948
|
-
}, lcAliases: {
|
|
949
|
-
[x: string]: string | undefined;
|
|
950
|
-
}): void;
|
|
951
|
-
setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
|
|
952
|
-
setLoadingP(p?: Promise<void> | undefined): void;
|
|
953
|
-
load(): Promise<void>;
|
|
954
|
-
loadPre(): Promise<void>;
|
|
955
|
-
} & {
|
|
956
|
-
getAdapterMapEntry(adapterConf: {
|
|
957
|
-
[x: string]: unknown;
|
|
958
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
|
|
959
|
-
getRefNameMapForAdapter(adapterConf: {
|
|
960
|
-
[x: string]: unknown;
|
|
961
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
962
|
-
[x: string]: string | undefined;
|
|
963
|
-
}>;
|
|
964
|
-
getReverseRefNameMapForAdapter(adapterConf: {
|
|
965
|
-
[x: string]: unknown;
|
|
966
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
967
|
-
[x: string]: string | undefined;
|
|
968
|
-
}>;
|
|
969
|
-
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
970
|
-
configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
|
|
971
|
-
}, {
|
|
972
|
-
error: unknown;
|
|
973
|
-
loaded: boolean;
|
|
974
|
-
loadingP: Promise<void> | undefined;
|
|
975
|
-
volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
976
|
-
refNameAliases: {
|
|
977
|
-
[x: string]: string | undefined;
|
|
978
|
-
} | undefined;
|
|
979
|
-
lowerCaseRefNameAliases: {
|
|
980
|
-
[x: string]: string | undefined;
|
|
981
|
-
} | undefined; /**
|
|
982
|
-
* #property
|
|
983
|
-
*/
|
|
984
|
-
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
985
|
-
} & {
|
|
986
|
-
getConf(arg: string): any;
|
|
987
|
-
} & {
|
|
988
|
-
readonly initialized: boolean;
|
|
989
|
-
readonly name: string;
|
|
990
|
-
readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
991
|
-
readonly aliases: string[];
|
|
992
|
-
readonly displayName: string | undefined;
|
|
993
|
-
hasName(name: string): boolean;
|
|
994
|
-
readonly allAliases: string[];
|
|
995
|
-
readonly allRefNames: string[] | undefined;
|
|
996
|
-
readonly lowerCaseRefNames: string[] | undefined;
|
|
997
|
-
readonly allRefNamesWithLowerCase: string[] | undefined;
|
|
998
|
-
readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
|
|
999
|
-
readonly refNameColors: string[];
|
|
1000
|
-
} & {
|
|
1001
|
-
readonly refNames: string[] | undefined;
|
|
1002
|
-
} & {
|
|
1003
|
-
getCanonicalRefName(refName: string): string | undefined;
|
|
1004
|
-
getRefNameColor(refName: string): string | undefined;
|
|
1005
|
-
isValidRefName(refName: string): boolean;
|
|
1006
|
-
} & {
|
|
1007
|
-
setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
|
|
1008
|
-
setError(e: unknown): void;
|
|
1009
|
-
setRegions(regions: import("@jbrowse/core/util").Region[]): void;
|
|
1010
|
-
setRefNameAliases(aliases: {
|
|
1011
|
-
[x: string]: string | undefined;
|
|
1012
|
-
}, lcAliases: {
|
|
1013
|
-
[x: string]: string | undefined;
|
|
1014
|
-
}): void;
|
|
1015
|
-
setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
|
|
1016
|
-
setLoadingP(p?: Promise<void> | undefined): void;
|
|
1017
|
-
load(): Promise<void>;
|
|
1018
|
-
loadPre(): Promise<void>;
|
|
1019
|
-
} & {
|
|
1020
|
-
getAdapterMapEntry(adapterConf: {
|
|
1021
|
-
[x: string]: unknown;
|
|
1022
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
|
|
1023
|
-
getRefNameMapForAdapter(adapterConf: {
|
|
1024
|
-
[x: string]: unknown;
|
|
1025
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
1026
|
-
[x: string]: string | undefined;
|
|
1027
|
-
}>;
|
|
1028
|
-
getReverseRefNameMapForAdapter(adapterConf: {
|
|
1029
|
-
[x: string]: unknown;
|
|
1030
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
1031
|
-
[x: string]: string | undefined;
|
|
1032
|
-
}>;
|
|
1033
|
-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
1034
|
-
}): Promise<void>;
|
|
1035
|
-
navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
|
|
1036
|
-
navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
|
|
1037
|
-
navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
|
|
1038
|
-
} & {
|
|
1039
|
-
rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
1040
|
-
bpToPx({ refName, coord, regionNumber, }: {
|
|
1041
|
-
refName: string;
|
|
1042
|
-
coord: number;
|
|
1043
|
-
regionNumber?: number | undefined;
|
|
1044
|
-
}): {
|
|
1045
|
-
index: number;
|
|
1046
|
-
offsetPx: number;
|
|
1047
|
-
} | undefined;
|
|
1048
|
-
centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
|
|
1049
|
-
pxToBp(px: number): {
|
|
1050
|
-
coord: number;
|
|
1051
|
-
index: number;
|
|
1052
|
-
refName: string;
|
|
1053
|
-
oob: boolean;
|
|
1054
|
-
assemblyName: string;
|
|
1055
|
-
offset: number;
|
|
1056
|
-
start: number;
|
|
1057
|
-
end: number;
|
|
1058
|
-
reversed?: boolean | undefined;
|
|
1059
|
-
};
|
|
1060
|
-
readonly centerLineInfo: {
|
|
1061
|
-
coord: number;
|
|
1062
|
-
index: number;
|
|
1063
|
-
refName: string;
|
|
1064
|
-
oob: boolean;
|
|
1065
|
-
assemblyName: string;
|
|
1066
|
-
offset: number;
|
|
1067
|
-
start: number;
|
|
1068
|
-
end: number;
|
|
1069
|
-
reversed?: boolean | undefined;
|
|
1070
|
-
} | undefined;
|
|
1071
|
-
} & {
|
|
1072
|
-
afterCreate(): void;
|
|
1073
|
-
}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
|
|
1074
|
-
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
1075
|
-
displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
1076
|
-
minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
1077
|
-
} & {
|
|
1078
|
-
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
1079
|
-
type: import("mobx-state-tree").IType<string | undefined, string, string>;
|
|
1080
|
-
offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
1081
|
-
bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
1082
|
-
displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
|
|
1083
|
-
tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
|
|
1084
|
-
hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
1085
|
-
hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
1086
|
-
hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
1087
|
-
trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
1088
|
-
showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
1089
|
-
showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
1090
|
-
trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
1091
|
-
showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
1092
|
-
highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
|
|
1093
|
-
colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
1094
|
-
}>>, import("mobx-state-tree")._NotCustomized>>): void;
|
|
279
|
+
setViews(views: import("mobx-state-tree").SnapshotIn<import("@jbrowse/plugin-linear-genome-view").LinearGenomeViewModel>[]): void;
|
|
280
|
+
removeView(view: import("@jbrowse/plugin-linear-genome-view").LinearGenomeViewModel): void;
|
|
1095
281
|
closeView(): void;
|
|
1096
282
|
setMiddleComparativeHeight(n: number): number;
|
|
1097
283
|
activateTrackSelector(): import("@jbrowse/core/util").Widget | undefined;
|