@jbrowse/product-core 5.0.0-beta.13 → 5.0.0-beta.14
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/esm/RootModel/BaseRootModel.d.ts +88 -47
- package/esm/RootModel/BaseRootModel.js +45 -2
- package/esm/RootModel/HierarchicalConfig.d.ts +3 -1
- package/esm/RootModel/HierarchicalConfig.js +3 -1
- package/esm/RootModel/InternetAccounts.d.ts +2 -0
- package/esm/RootModel/InternetAccounts.js +2 -0
- package/esm/RootModel/PreferencesConfig.d.ts +4 -4
- package/esm/RootModel/PreferencesConfig.js +4 -4
- package/esm/RootModel/menuItems.d.ts +1 -2
- package/esm/RootModel/menuItems.js +3 -4
- package/esm/Session/BaseSession.d.ts +7 -5
- package/esm/Session/BaseSession.js +15 -5
- package/esm/Session/Connections.d.ts +3 -0
- package/esm/Session/Connections.js +3 -0
- package/esm/Session/DrawerWidgets.d.ts +2 -0
- package/esm/Session/DrawerWidgets.js +2 -0
- package/esm/Session/MultipleViews.d.ts +122 -96
- package/esm/Session/MultipleViews.js +5 -3
- package/esm/Session/Preferences.d.ts +122 -97
- package/esm/Session/Preferences.js +5 -4
- package/esm/Session/ReferenceManagement.d.ts +2 -0
- package/esm/Session/ReferenceManagement.js +2 -0
- package/esm/Session/SessionTracks.d.ts +119 -93
- package/esm/Session/SessionTracks.js +2 -0
- package/esm/Session/Themes.d.ts +7 -5
- package/esm/Session/Themes.js +15 -10
- package/esm/Session/TrackMenu.d.ts +4 -8
- package/esm/Session/TrackMenu.js +13 -7
- package/esm/Session/TrackMenuSessionMixin.js +7 -3
- package/esm/Session/Tracks.d.ts +120 -93
- package/esm/Session/Tracks.js +3 -0
- package/esm/Session/pluginExtraTrackItems.d.ts +2 -3
- package/esm/Session/pluginExtraTrackItems.js +1 -1
- package/esm/sessionMigrations/index.js +2 -2
- package/esm/siblingCast.d.ts +6 -0
- package/esm/siblingCast.js +7 -0
- package/esm/ui/AboutDialog.d.ts +3 -2
- package/esm/ui/AboutDialog.js +4 -2
- package/esm/ui/DescriptionPanel.js +4 -4
- package/esm/ui/Drawer.js +11 -15
- package/esm/ui/HeaderButtons.d.ts +1 -1
- package/esm/ui/HeaderButtons.js +3 -2
- package/esm/ui/PreferenceCheckbox.d.ts +3 -2
- package/esm/ui/PreferenceCheckbox.js +4 -2
- package/esm/ui/WidgetHeading.d.ts +2 -2
- package/esm/ui/WidgetHeading.js +3 -2
- package/package.json +6 -6
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@@ -4,6 +4,8 @@ import type { IBaseViewModel } from '@jbrowse/core/pluggableElementTypes';
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import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
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/**
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* #stateModel MultipleViewsSessionMixin
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* Adds a list of views to a session, with actions to add, remove, replace and
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* reorder them.
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*/
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export declare function MultipleViewsSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{
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id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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@@ -44,13 +46,13 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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}, {
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error: unknown;
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loadingP: Promise<void> | undefined;
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adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
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adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
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regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: import("@jbrowse/core/assemblyManager/
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refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
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cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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loadedGeneticCodes: Record<string, number> | undefined;
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lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
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lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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statusMessage: string | undefined;
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statusProgress: number | undefined;
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statusSource: string | undefined;
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@@ -69,7 +71,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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} & {
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setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
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setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
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regions: import("@jbrowse/core/util").Region[];
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cytobands: import("@jbrowse/core/util").Feature[];
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geneticCodes: Record<string, number>;
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getCanonicalRefName2(refName: string): string;
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isValidRefName(refName: string): boolean;
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} & {
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isCircularRefName(refName: string): boolean;
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getRefNamePosition(refName: string): number | undefined;
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getAliasesForRefName(refName: string): string[];
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getRefNameMapForAdapter(adapterConf: {
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[x: string]: unknown;
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
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getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
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}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
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}, {
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@@ -125,13 +128,13 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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}> & {
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error: unknown;
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loadingP: Promise<void> | undefined;
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adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
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adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
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regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: import("@jbrowse/core/assemblyManager/
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refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
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cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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loadedGeneticCodes: Record<string, number> | undefined;
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lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
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lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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statusMessage: string | undefined;
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statusProgress: number | undefined;
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statusSource: string | undefined;
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@@ -150,7 +153,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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} & {
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setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
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setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
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regions: import("@jbrowse/core/util").Region[];
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cytobands: import("@jbrowse/core/util").Feature[];
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geneticCodes: Record<string, number>;
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@@ -181,24 +184,25 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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getCanonicalRefName2(refName: string): string;
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isValidRefName(refName: string): boolean;
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} & {
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isCircularRefName(refName: string): boolean;
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getRefNamePosition(refName: string): number | undefined;
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getAliasesForRefName(refName: string): string[];
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getRefNameMapForAdapter(adapterConf: {
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[x: string]: unknown;
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
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getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
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} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
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configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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}, {
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error: unknown;
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loadingP: Promise<void> | undefined;
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adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
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adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
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regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: import("@jbrowse/core/assemblyManager/
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refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
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cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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loadedGeneticCodes: Record<string, number> | undefined;
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lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
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lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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statusMessage: string | undefined;
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statusProgress: number | undefined;
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statusSource: string | undefined;
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setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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} & {
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setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
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setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
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regions: import("@jbrowse/core/util").Region[];
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getCanonicalRefName2(refName: string): string;
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isValidRefName(refName: string): boolean;
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isCircularRefName(refName: string): boolean;
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getRefNamePosition(refName: string): number | undefined;
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getAliasesForRefName(refName: string): string[];
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
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getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
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}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
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has(asmName: string): boolean;
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loadingP: Promise<void> | undefined;
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adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
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adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
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regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: import("@jbrowse/core/assemblyManager/
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refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
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cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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loadedGeneticCodes: Record<string, number> | undefined;
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lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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statusMessage: string | undefined;
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statusProgress: number | undefined;
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statusSource: string | undefined;
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setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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} & {
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setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
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setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
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regions: import("@jbrowse/core/util").Region[];
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cytobands: import("@jbrowse/core/util").Feature[];
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getRefNamePosition(refName: string): number | undefined;
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
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getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
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} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
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configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
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regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: import("@jbrowse/core/assemblyManager/
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refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
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cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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loadedGeneticCodes: Record<string, number> | undefined;
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lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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statusMessage: string | undefined;
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statusProgress: number | undefined;
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statusSource: string | undefined;
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setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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} & {
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setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
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setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
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|
regions: import("@jbrowse/core/util").Region[];
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cytobands: import("@jbrowse/core/util").Feature[];
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geneticCodes: Record<string, number>;
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@@ -384,11 +390,12 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
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384
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getCanonicalRefName2(refName: string): string;
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385
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|
isValidRefName(refName: string): boolean;
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386
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} & {
|
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393
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+
isCircularRefName(refName: string): boolean;
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387
394
|
getRefNamePosition(refName: string): number | undefined;
|
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395
|
getAliasesForRefName(refName: string): string[];
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getRefNameMapForAdapter(adapterConf: {
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[x: string]: unknown;
|
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391
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
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398
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+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
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getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
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}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
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readonly assemblyNamesList: string[];
|
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@@ -403,13 +410,13 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
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}> & {
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404
411
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error: unknown;
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412
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loadingP: Promise<void> | undefined;
|
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406
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
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413
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
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407
414
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regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
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408
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
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415
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
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409
416
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
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410
417
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cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
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411
418
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loadedGeneticCodes: Record<string, number> | undefined;
|
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412
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
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419
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
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statusMessage: string | undefined;
|
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414
421
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statusProgress: number | undefined;
|
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statusSource: string | undefined;
|
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@@ -428,7 +435,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
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428
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|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
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429
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|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
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430
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|
} & {
|
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431
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
438
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
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432
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|
regions: import("@jbrowse/core/util").Region[];
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cytobands: import("@jbrowse/core/util").Feature[];
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geneticCodes: Record<string, number>;
|
|
@@ -459,24 +466,25 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
459
466
|
getCanonicalRefName2(refName: string): string;
|
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460
467
|
isValidRefName(refName: string): boolean;
|
|
461
468
|
} & {
|
|
469
|
+
isCircularRefName(refName: string): boolean;
|
|
462
470
|
getRefNamePosition(refName: string): number | undefined;
|
|
463
471
|
getAliasesForRefName(refName: string): string[];
|
|
464
472
|
getRefNameMapForAdapter(adapterConf: {
|
|
465
473
|
[x: string]: unknown;
|
|
466
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
474
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
467
475
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
468
476
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
469
477
|
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
470
478
|
}, {
|
|
471
479
|
error: unknown;
|
|
472
480
|
loadingP: Promise<void> | undefined;
|
|
473
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
481
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
474
482
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
475
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
483
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
476
484
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
477
485
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
478
486
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
479
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
487
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
480
488
|
statusMessage: string | undefined;
|
|
481
489
|
statusProgress: number | undefined;
|
|
482
490
|
statusSource: string | undefined;
|
|
@@ -495,7 +503,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
495
503
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
496
504
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
497
505
|
} & {
|
|
498
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
506
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
499
507
|
regions: import("@jbrowse/core/util").Region[];
|
|
500
508
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
501
509
|
geneticCodes: Record<string, number>;
|
|
@@ -526,11 +534,12 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
526
534
|
getCanonicalRefName2(refName: string): string;
|
|
527
535
|
isValidRefName(refName: string): boolean;
|
|
528
536
|
} & {
|
|
537
|
+
isCircularRefName(refName: string): boolean;
|
|
529
538
|
getRefNamePosition(refName: string): number | undefined;
|
|
530
539
|
getAliasesForRefName(refName: string): string[];
|
|
531
540
|
getRefNameMapForAdapter(adapterConf: {
|
|
532
541
|
[x: string]: unknown;
|
|
533
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
542
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
534
543
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
535
544
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
|
|
536
545
|
requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
@@ -538,13 +547,13 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
538
547
|
}> & {
|
|
539
548
|
error: unknown;
|
|
540
549
|
loadingP: Promise<void> | undefined;
|
|
541
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
550
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
542
551
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
543
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
552
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
544
553
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
545
554
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
546
555
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
547
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
556
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
548
557
|
statusMessage: string | undefined;
|
|
549
558
|
statusProgress: number | undefined;
|
|
550
559
|
statusSource: string | undefined;
|
|
@@ -563,7 +572,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
563
572
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
564
573
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
565
574
|
} & {
|
|
566
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
575
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
567
576
|
regions: import("@jbrowse/core/util").Region[];
|
|
568
577
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
569
578
|
geneticCodes: Record<string, number>;
|
|
@@ -594,24 +603,25 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
594
603
|
getCanonicalRefName2(refName: string): string;
|
|
595
604
|
isValidRefName(refName: string): boolean;
|
|
596
605
|
} & {
|
|
606
|
+
isCircularRefName(refName: string): boolean;
|
|
597
607
|
getRefNamePosition(refName: string): number | undefined;
|
|
598
608
|
getAliasesForRefName(refName: string): string[];
|
|
599
609
|
getRefNameMapForAdapter(adapterConf: {
|
|
600
610
|
[x: string]: unknown;
|
|
601
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
611
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
602
612
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
603
613
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
604
614
|
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
605
615
|
}, {
|
|
606
616
|
error: unknown;
|
|
607
617
|
loadingP: Promise<void> | undefined;
|
|
608
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
618
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
609
619
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
610
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
620
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
611
621
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
612
622
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
613
623
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
614
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
624
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
615
625
|
statusMessage: string | undefined;
|
|
616
626
|
statusProgress: number | undefined;
|
|
617
627
|
statusSource: string | undefined;
|
|
@@ -630,7 +640,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
630
640
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
631
641
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
632
642
|
} & {
|
|
633
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
643
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
634
644
|
regions: import("@jbrowse/core/util").Region[];
|
|
635
645
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
636
646
|
geneticCodes: Record<string, number>;
|
|
@@ -661,16 +671,17 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
661
671
|
getCanonicalRefName2(refName: string): string;
|
|
662
672
|
isValidRefName(refName: string): boolean;
|
|
663
673
|
} & {
|
|
674
|
+
isCircularRefName(refName: string): boolean;
|
|
664
675
|
getRefNamePosition(refName: string): number | undefined;
|
|
665
676
|
getAliasesForRefName(refName: string): string[];
|
|
666
677
|
getRefNameMapForAdapter(adapterConf: {
|
|
667
678
|
[x: string]: unknown;
|
|
668
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
679
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
669
680
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
670
681
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
|
|
671
682
|
getRefNameMapForAdapter(adapterConf: {
|
|
672
683
|
[x: string]: unknown;
|
|
673
|
-
}, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/
|
|
684
|
+
}, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
674
685
|
isValidRefName(refName: string, assemblyName: string): boolean;
|
|
675
686
|
} & {
|
|
676
687
|
afterAttach(): void;
|
|
@@ -683,8 +694,11 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
683
694
|
error: unknown;
|
|
684
695
|
textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
|
|
685
696
|
pluginManager: PluginManager;
|
|
697
|
+
detachDisposers: (() => void)[];
|
|
686
698
|
} & {
|
|
687
699
|
setError(error: unknown): void;
|
|
700
|
+
addDetachDisposer(disposer: () => void): void;
|
|
701
|
+
detach(): void;
|
|
688
702
|
setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
|
|
689
703
|
setDefaultSession(): void;
|
|
690
704
|
setSessionPath(path: string): void;
|
|
@@ -699,13 +713,13 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
699
713
|
}, {
|
|
700
714
|
error: unknown;
|
|
701
715
|
loadingP: Promise<void> | undefined;
|
|
702
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
716
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
703
717
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
704
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
718
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
705
719
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
706
720
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
707
721
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
708
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
722
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
709
723
|
statusMessage: string | undefined;
|
|
710
724
|
statusProgress: number | undefined;
|
|
711
725
|
statusSource: string | undefined;
|
|
@@ -724,7 +738,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
724
738
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
725
739
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
726
740
|
} & {
|
|
727
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
741
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
728
742
|
regions: import("@jbrowse/core/util").Region[];
|
|
729
743
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
730
744
|
geneticCodes: Record<string, number>;
|
|
@@ -755,11 +769,12 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
755
769
|
getCanonicalRefName2(refName: string): string;
|
|
756
770
|
isValidRefName(refName: string): boolean;
|
|
757
771
|
} & {
|
|
772
|
+
isCircularRefName(refName: string): boolean;
|
|
758
773
|
getRefNamePosition(refName: string): number | undefined;
|
|
759
774
|
getAliasesForRefName(refName: string): string[];
|
|
760
775
|
getRefNameMapForAdapter(adapterConf: {
|
|
761
776
|
[x: string]: unknown;
|
|
762
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
777
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
763
778
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
764
779
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
|
|
765
780
|
}, {
|
|
@@ -780,13 +795,13 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
780
795
|
}> & {
|
|
781
796
|
error: unknown;
|
|
782
797
|
loadingP: Promise<void> | undefined;
|
|
783
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
798
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
784
799
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
785
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
800
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
786
801
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
787
802
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
788
803
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
789
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
804
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
790
805
|
statusMessage: string | undefined;
|
|
791
806
|
statusProgress: number | undefined;
|
|
792
807
|
statusSource: string | undefined;
|
|
@@ -805,7 +820,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
805
820
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
806
821
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
807
822
|
} & {
|
|
808
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
823
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
809
824
|
regions: import("@jbrowse/core/util").Region[];
|
|
810
825
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
811
826
|
geneticCodes: Record<string, number>;
|
|
@@ -836,24 +851,25 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
836
851
|
getCanonicalRefName2(refName: string): string;
|
|
837
852
|
isValidRefName(refName: string): boolean;
|
|
838
853
|
} & {
|
|
854
|
+
isCircularRefName(refName: string): boolean;
|
|
839
855
|
getRefNamePosition(refName: string): number | undefined;
|
|
840
856
|
getAliasesForRefName(refName: string): string[];
|
|
841
857
|
getRefNameMapForAdapter(adapterConf: {
|
|
842
858
|
[x: string]: unknown;
|
|
843
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
859
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
844
860
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
845
861
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
846
862
|
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
847
863
|
}, {
|
|
848
864
|
error: unknown;
|
|
849
865
|
loadingP: Promise<void> | undefined;
|
|
850
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
866
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
851
867
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
852
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
868
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
853
869
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
854
870
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
855
871
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
856
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
872
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
857
873
|
statusMessage: string | undefined;
|
|
858
874
|
statusProgress: number | undefined;
|
|
859
875
|
statusSource: string | undefined;
|
|
@@ -872,7 +888,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
872
888
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
873
889
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
874
890
|
} & {
|
|
875
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
891
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
876
892
|
regions: import("@jbrowse/core/util").Region[];
|
|
877
893
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
878
894
|
geneticCodes: Record<string, number>;
|
|
@@ -903,11 +919,12 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
903
919
|
getCanonicalRefName2(refName: string): string;
|
|
904
920
|
isValidRefName(refName: string): boolean;
|
|
905
921
|
} & {
|
|
922
|
+
isCircularRefName(refName: string): boolean;
|
|
906
923
|
getRefNamePosition(refName: string): number | undefined;
|
|
907
924
|
getAliasesForRefName(refName: string): string[];
|
|
908
925
|
getRefNameMapForAdapter(adapterConf: {
|
|
909
926
|
[x: string]: unknown;
|
|
910
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
927
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
911
928
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
912
929
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
|
|
913
930
|
has(asmName: string): boolean;
|
|
@@ -916,13 +933,13 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
916
933
|
}> & {
|
|
917
934
|
error: unknown;
|
|
918
935
|
loadingP: Promise<void> | undefined;
|
|
919
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
936
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
920
937
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
921
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
938
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
922
939
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
923
940
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
924
941
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
925
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
942
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
926
943
|
statusMessage: string | undefined;
|
|
927
944
|
statusProgress: number | undefined;
|
|
928
945
|
statusSource: string | undefined;
|
|
@@ -941,7 +958,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
941
958
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
942
959
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
943
960
|
} & {
|
|
944
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
961
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
945
962
|
regions: import("@jbrowse/core/util").Region[];
|
|
946
963
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
947
964
|
geneticCodes: Record<string, number>;
|
|
@@ -972,24 +989,25 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
972
989
|
getCanonicalRefName2(refName: string): string;
|
|
973
990
|
isValidRefName(refName: string): boolean;
|
|
974
991
|
} & {
|
|
992
|
+
isCircularRefName(refName: string): boolean;
|
|
975
993
|
getRefNamePosition(refName: string): number | undefined;
|
|
976
994
|
getAliasesForRefName(refName: string): string[];
|
|
977
995
|
getRefNameMapForAdapter(adapterConf: {
|
|
978
996
|
[x: string]: unknown;
|
|
979
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
997
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
980
998
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
981
999
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
982
1000
|
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
983
1001
|
}, {
|
|
984
1002
|
error: unknown;
|
|
985
1003
|
loadingP: Promise<void> | undefined;
|
|
986
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
1004
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
987
1005
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
988
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
1006
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
989
1007
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
990
1008
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
991
1009
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
992
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
1010
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
993
1011
|
statusMessage: string | undefined;
|
|
994
1012
|
statusProgress: number | undefined;
|
|
995
1013
|
statusSource: string | undefined;
|
|
@@ -1008,7 +1026,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1008
1026
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1009
1027
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1010
1028
|
} & {
|
|
1011
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
1029
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
1012
1030
|
regions: import("@jbrowse/core/util").Region[];
|
|
1013
1031
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1014
1032
|
geneticCodes: Record<string, number>;
|
|
@@ -1039,11 +1057,12 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1039
1057
|
getCanonicalRefName2(refName: string): string;
|
|
1040
1058
|
isValidRefName(refName: string): boolean;
|
|
1041
1059
|
} & {
|
|
1060
|
+
isCircularRefName(refName: string): boolean;
|
|
1042
1061
|
getRefNamePosition(refName: string): number | undefined;
|
|
1043
1062
|
getAliasesForRefName(refName: string): string[];
|
|
1044
1063
|
getRefNameMapForAdapter(adapterConf: {
|
|
1045
1064
|
[x: string]: unknown;
|
|
1046
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
1065
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
1047
1066
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1048
1067
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
|
|
1049
1068
|
readonly assemblyNamesList: string[];
|
|
@@ -1058,13 +1077,13 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1058
1077
|
}> & {
|
|
1059
1078
|
error: unknown;
|
|
1060
1079
|
loadingP: Promise<void> | undefined;
|
|
1061
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
1080
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
1062
1081
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1063
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
1082
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
1064
1083
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1065
1084
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1066
1085
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1067
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
1086
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
1068
1087
|
statusMessage: string | undefined;
|
|
1069
1088
|
statusProgress: number | undefined;
|
|
1070
1089
|
statusSource: string | undefined;
|
|
@@ -1083,7 +1102,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1083
1102
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1084
1103
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1085
1104
|
} & {
|
|
1086
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
1105
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
1087
1106
|
regions: import("@jbrowse/core/util").Region[];
|
|
1088
1107
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1089
1108
|
geneticCodes: Record<string, number>;
|
|
@@ -1114,24 +1133,25 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1114
1133
|
getCanonicalRefName2(refName: string): string;
|
|
1115
1134
|
isValidRefName(refName: string): boolean;
|
|
1116
1135
|
} & {
|
|
1136
|
+
isCircularRefName(refName: string): boolean;
|
|
1117
1137
|
getRefNamePosition(refName: string): number | undefined;
|
|
1118
1138
|
getAliasesForRefName(refName: string): string[];
|
|
1119
1139
|
getRefNameMapForAdapter(adapterConf: {
|
|
1120
1140
|
[x: string]: unknown;
|
|
1121
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
1141
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
1122
1142
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1123
1143
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
1124
1144
|
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
1125
1145
|
}, {
|
|
1126
1146
|
error: unknown;
|
|
1127
1147
|
loadingP: Promise<void> | undefined;
|
|
1128
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
1148
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
1129
1149
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1130
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
1150
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
1131
1151
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1132
1152
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1133
1153
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1134
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
1154
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
1135
1155
|
statusMessage: string | undefined;
|
|
1136
1156
|
statusProgress: number | undefined;
|
|
1137
1157
|
statusSource: string | undefined;
|
|
@@ -1150,7 +1170,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1150
1170
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1151
1171
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1152
1172
|
} & {
|
|
1153
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
1173
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
1154
1174
|
regions: import("@jbrowse/core/util").Region[];
|
|
1155
1175
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1156
1176
|
geneticCodes: Record<string, number>;
|
|
@@ -1181,11 +1201,12 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1181
1201
|
getCanonicalRefName2(refName: string): string;
|
|
1182
1202
|
isValidRefName(refName: string): boolean;
|
|
1183
1203
|
} & {
|
|
1204
|
+
isCircularRefName(refName: string): boolean;
|
|
1184
1205
|
getRefNamePosition(refName: string): number | undefined;
|
|
1185
1206
|
getAliasesForRefName(refName: string): string[];
|
|
1186
1207
|
getRefNameMapForAdapter(adapterConf: {
|
|
1187
1208
|
[x: string]: unknown;
|
|
1188
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
1209
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
1189
1210
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1190
1211
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
|
|
1191
1212
|
requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
@@ -1193,13 +1214,13 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1193
1214
|
}> & {
|
|
1194
1215
|
error: unknown;
|
|
1195
1216
|
loadingP: Promise<void> | undefined;
|
|
1196
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
1217
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
1197
1218
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1198
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
1219
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
1199
1220
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1200
1221
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1201
1222
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1202
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
1223
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
1203
1224
|
statusMessage: string | undefined;
|
|
1204
1225
|
statusProgress: number | undefined;
|
|
1205
1226
|
statusSource: string | undefined;
|
|
@@ -1218,7 +1239,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1218
1239
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1219
1240
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1220
1241
|
} & {
|
|
1221
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
1242
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
1222
1243
|
regions: import("@jbrowse/core/util").Region[];
|
|
1223
1244
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1224
1245
|
geneticCodes: Record<string, number>;
|
|
@@ -1249,24 +1270,25 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1249
1270
|
getCanonicalRefName2(refName: string): string;
|
|
1250
1271
|
isValidRefName(refName: string): boolean;
|
|
1251
1272
|
} & {
|
|
1273
|
+
isCircularRefName(refName: string): boolean;
|
|
1252
1274
|
getRefNamePosition(refName: string): number | undefined;
|
|
1253
1275
|
getAliasesForRefName(refName: string): string[];
|
|
1254
1276
|
getRefNameMapForAdapter(adapterConf: {
|
|
1255
1277
|
[x: string]: unknown;
|
|
1256
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
1278
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
1257
1279
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1258
1280
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
1259
1281
|
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
1260
1282
|
}, {
|
|
1261
1283
|
error: unknown;
|
|
1262
1284
|
loadingP: Promise<void> | undefined;
|
|
1263
|
-
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/
|
|
1285
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
|
|
1264
1286
|
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1265
|
-
refNameAliases: import("@jbrowse/core/assemblyManager/
|
|
1287
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
1266
1288
|
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1267
1289
|
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1268
1290
|
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1269
|
-
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/
|
|
1291
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
|
|
1270
1292
|
statusMessage: string | undefined;
|
|
1271
1293
|
statusProgress: number | undefined;
|
|
1272
1294
|
statusSource: string | undefined;
|
|
@@ -1285,7 +1307,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1285
1307
|
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1286
1308
|
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1287
1309
|
} & {
|
|
1288
|
-
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/
|
|
1310
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
|
|
1289
1311
|
regions: import("@jbrowse/core/util").Region[];
|
|
1290
1312
|
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1291
1313
|
geneticCodes: Record<string, number>;
|
|
@@ -1316,16 +1338,17 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1316
1338
|
getCanonicalRefName2(refName: string): string;
|
|
1317
1339
|
isValidRefName(refName: string): boolean;
|
|
1318
1340
|
} & {
|
|
1341
|
+
isCircularRefName(refName: string): boolean;
|
|
1319
1342
|
getRefNamePosition(refName: string): number | undefined;
|
|
1320
1343
|
getAliasesForRefName(refName: string): string[];
|
|
1321
1344
|
getRefNameMapForAdapter(adapterConf: {
|
|
1322
1345
|
[x: string]: unknown;
|
|
1323
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/
|
|
1346
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
1324
1347
|
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1325
1348
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
|
|
1326
1349
|
getRefNameMapForAdapter(adapterConf: {
|
|
1327
1350
|
[x: string]: unknown;
|
|
1328
|
-
}, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/
|
|
1351
|
+
}, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
|
|
1329
1352
|
isValidRefName(refName: string, assemblyName: string): boolean;
|
|
1330
1353
|
} & {
|
|
1331
1354
|
afterAttach(): void;
|
|
@@ -1338,8 +1361,11 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1338
1361
|
error: unknown;
|
|
1339
1362
|
textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
|
|
1340
1363
|
pluginManager: PluginManager;
|
|
1364
|
+
detachDisposers: (() => void)[];
|
|
1341
1365
|
} & {
|
|
1342
1366
|
setError(error: unknown): void;
|
|
1367
|
+
addDetachDisposer(disposer: () => void): void;
|
|
1368
|
+
detach(): void;
|
|
1343
1369
|
setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
|
|
1344
1370
|
setDefaultSession(): void;
|
|
1345
1371
|
setSessionPath(path: string): void;
|
|
@@ -1381,7 +1407,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1381
1407
|
setName(str: string): void;
|
|
1382
1408
|
setFocusedViewId(viewId: string | undefined): void;
|
|
1383
1409
|
removeActiveDialog(): void;
|
|
1384
|
-
queueDialog(
|
|
1410
|
+
queueDialog<T extends import("@jbrowse/core/util").DialogComponentType>(callback: (doneCallback: () => void) => [T, import("react").ComponentProps<T>]): void;
|
|
1385
1411
|
removeDialog(entry: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
|
|
1386
1412
|
} & {
|
|
1387
1413
|
snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
|
|
@@ -1481,9 +1507,9 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
|
|
|
1481
1507
|
* and so lets its snackbar offer an Undo. Swapping in a new node would
|
|
1482
1508
|
* leave nothing to undo onto.
|
|
1483
1509
|
*
|
|
1484
|
-
* The slot is `session.views`,
|
|
1485
|
-
*
|
|
1486
|
-
*
|
|
1510
|
+
* The slot is `session.views`, the order views render in (a tab's
|
|
1511
|
+
* `viewIds` says which tab a view is in, not where in it), so the swap
|
|
1512
|
+
* lands in place.
|
|
1487
1513
|
*
|
|
1488
1514
|
* WHICH panel is a separate question and this does not answer it: the
|
|
1489
1515
|
* new view arrives in no tab, and `homeUnassignedViews` puts it in the
|