@jbrowse/product-core 2.9.0 → 2.10.1
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/RootModel/BaseRootModel.d.ts +102 -56
- package/dist/Session/BaseSession.d.ts +11 -3
- package/dist/Session/BaseSession.js +5 -1
- package/dist/Session/MultipleViews.d.ts +301 -110
- package/dist/Session/MultipleViews.js +3 -0
- package/dist/Session/SessionTracks.d.ts +285 -117
- package/dist/Session/Tracks.d.ts +304 -98
- package/esm/RootModel/BaseRootModel.d.ts +102 -56
- package/esm/Session/BaseSession.d.ts +11 -3
- package/esm/Session/BaseSession.js +5 -1
- package/esm/Session/MultipleViews.d.ts +301 -110
- package/esm/Session/MultipleViews.js +3 -0
- package/esm/Session/SessionTracks.d.ts +285 -117
- package/esm/Session/Tracks.d.ts +304 -98
- package/package.json +3 -3
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@@ -56,10 +56,14 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
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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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hasName(name: string): boolean; /**
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* #action
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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 lowerCaseRefNames: string[] | undefined; /**
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* #action
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*/
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readonly allRefNamesWithLowerCase: string[] | undefined;
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readonly rpcManager: RpcManager;
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readonly refNameColors: string[];
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@@ -72,9 +76,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
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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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* #action
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*/
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setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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setRefNameAliases(aliases: {
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[x: string]: string | undefined;
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}, lcAliases: {
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@@ -85,11 +87,17 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
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load(): Promise<void>;
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loadPre(): Promise<void>;
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} & {
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getAdapterMapEntry(adapterConf:
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getAdapterMapEntry(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/assembly").RefNameMap>;
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getRefNameMapForAdapter(adapterConf: {
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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[x: string]: string | undefined;
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}>;
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getReverseRefNameMapForAdapter(adapterConf:
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getReverseRefNameMapForAdapter(adapterConf: {
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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[x: string]: string | undefined;
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}>;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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@@ -143,11 +151,17 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
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load(): Promise<void>;
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loadPre(): Promise<void>;
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} & {
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getAdapterMapEntry(adapterConf:
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getAdapterMapEntry(adapterConf: {
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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getRefNameMapForAdapter(adapterConf: {
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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}>;
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getReverseRefNameMapForAdapter(adapterConf:
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getReverseRefNameMapForAdapter(adapterConf: {
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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[x: string]: string | undefined;
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}>;
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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load(): Promise<void>;
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loadPre(): Promise<void>;
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} & {
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getAdapterMapEntry(adapterConf:
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getAdapterMapEntry(adapterConf: {
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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getRefNameMapForAdapter(adapterConf: {
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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}>;
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getReverseRefNameMapForAdapter(adapterConf:
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getReverseRefNameMapForAdapter(adapterConf: {
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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>>) | undefined>;
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@@ -257,11 +277,17 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
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load(): Promise<void>;
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loadPre(): Promise<void>;
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} & {
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getAdapterMapEntry(adapterConf:
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getAdapterMapEntry(adapterConf: {
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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getRefNameMapForAdapter(adapterConf: {
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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}>;
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getReverseRefNameMapForAdapter(adapterConf:
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getReverseRefNameMapForAdapter(adapterConf: {
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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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load(): Promise<void>;
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loadPre(): Promise<void>;
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} & {
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getAdapterMapEntry(adapterConf:
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getAdapterMapEntry(adapterConf: {
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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getRefNameMapForAdapter(adapterConf: {
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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}>;
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getReverseRefNameMapForAdapter(adapterConf:
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getReverseRefNameMapForAdapter(adapterConf: {
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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>>) | undefined;
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load(): Promise<void>;
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loadPre(): Promise<void>;
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} & {
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getAdapterMapEntry(adapterConf:
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getAdapterMapEntry(adapterConf: {
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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getRefNameMapForAdapter(adapterConf: {
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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}>;
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getReverseRefNameMapForAdapter(adapterConf:
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getReverseRefNameMapForAdapter(adapterConf: {
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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load(): Promise<void>;
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loadPre(): Promise<void>;
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} & {
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getAdapterMapEntry(adapterConf: {
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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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getReverseRefNameMapForAdapter(adapterConf: {
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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>>) | undefined>;
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getRefNameMapForAdapter(adapterConf: {
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}, assemblyName: string | undefined, opts: {
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signal?: AbortSignal | undefined;
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sessionId: string;
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}): Promise<{
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} | undefined>;
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getReverseRefNameMapForAdapter(adapterConf: {
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}, assemblyName: string | undefined, opts: {
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}): Promise<{
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removeAssembly(asm: {
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configuration: any;
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} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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* #property
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* `session` encompasses the currently active state of the app, including
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* views open, tracks open in those views, etc.
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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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} | undefined;
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} | undefined;
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} & {
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getConf(arg: string): any;
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readonly lowerCaseRefNames: string[] | undefined;
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readonly allRefNamesWithLowerCase: string[] | undefined;
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readonly rpcManager: RpcManager;
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readonly refNameColors: string[];
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* #action
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} & {
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isValidRefName(refName: string): boolean;
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} & {
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setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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setRefNameAliases(aliases: {
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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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} & 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<IAnyType>>;
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}, {
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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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} | undefined;
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} | undefined;
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} & {
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getConf(arg: string): any;
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@@ -555,9 +596,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
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555
596
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readonly lowerCaseRefNames: string[] | undefined;
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556
597
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readonly allRefNamesWithLowerCase: string[] | undefined;
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557
598
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readonly rpcManager: RpcManager;
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558
|
-
readonly refNameColors: string[];
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559
|
-
* #action
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560
|
-
*/
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599
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+
readonly refNameColors: string[];
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561
600
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} & {
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562
601
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readonly refNames: string[] | undefined;
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563
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} & {
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@@ -566,6 +605,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
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566
605
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isValidRefName(refName: string): boolean;
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567
606
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} & {
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568
607
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setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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608
|
+
/** Type guard for checking if something is a JB root model */
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569
609
|
setError(e: unknown): void;
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570
610
|
setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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571
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setRefNameAliases(aliases: {
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@@ -578,11 +618,17 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
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578
618
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load(): Promise<void>;
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579
619
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loadPre(): Promise<void>;
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580
620
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} & {
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581
|
-
getAdapterMapEntry(adapterConf:
|
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582
|
-
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|
621
|
+
getAdapterMapEntry(adapterConf: {
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622
|
+
[x: string]: unknown;
|
|
623
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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624
|
+
getRefNameMapForAdapter(adapterConf: {
|
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625
|
+
[x: string]: unknown;
|
|
626
|
+
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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583
627
|
[x: string]: string | undefined;
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|
584
628
|
}>;
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585
|
-
getReverseRefNameMapForAdapter(adapterConf:
|
|
629
|
+
getReverseRefNameMapForAdapter(adapterConf: {
|
|
630
|
+
[x: string]: unknown;
|
|
631
|
+
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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586
632
|
[x: string]: string | undefined;
|
|
587
633
|
}>;
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588
634
|
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
|
|
@@ -4,7 +4,8 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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4
4
|
import type { BaseRootModelType } from '../RootModel/BaseRootModel';
|
|
5
5
|
/**
|
|
6
6
|
* #stateModel BaseSessionModel
|
|
7
|
-
*
|
|
7
|
+
*
|
|
8
|
+
* base session shared by all JBrowse products. Be careful what you include
|
|
8
9
|
* here, everything will use it.
|
|
9
10
|
*/
|
|
10
11
|
export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelType, JB_CONFIG_SCHEMA extends AnyConfigurationSchemaType>(_pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
|
|
@@ -27,6 +28,9 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
|
|
|
27
28
|
*/
|
|
28
29
|
hovered: unknown;
|
|
29
30
|
} & {
|
|
31
|
+
/**
|
|
32
|
+
* #getter
|
|
33
|
+
*/
|
|
30
34
|
readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
|
|
31
35
|
} & {
|
|
32
36
|
/**
|
|
@@ -73,8 +77,12 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
|
|
|
73
77
|
adapter: import("mobx-state-tree").IAnyModelType;
|
|
74
78
|
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
75
79
|
cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
76
|
-
adapter: import("mobx-state-tree").IAnyModelType;
|
|
77
|
-
|
|
80
|
+
adapter: import("mobx-state-tree").IAnyModelType; /**
|
|
81
|
+
* #getter
|
|
82
|
+
*/
|
|
83
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>; /**
|
|
84
|
+
* #getter
|
|
85
|
+
*/
|
|
78
86
|
displayName: {
|
|
79
87
|
type: string;
|
|
80
88
|
defaultValue: string;
|
|
@@ -5,7 +5,8 @@ const mobx_state_tree_1 = require("mobx-state-tree");
|
|
|
5
5
|
const mst_1 = require("@jbrowse/core/util/types/mst");
|
|
6
6
|
/**
|
|
7
7
|
* #stateModel BaseSessionModel
|
|
8
|
-
*
|
|
8
|
+
*
|
|
9
|
+
* base session shared by all JBrowse products. Be careful what you include
|
|
9
10
|
* here, everything will use it.
|
|
10
11
|
*/
|
|
11
12
|
function BaseSessionModel(_pluginManager) {
|
|
@@ -41,6 +42,9 @@ function BaseSessionModel(_pluginManager) {
|
|
|
41
42
|
hovered: undefined,
|
|
42
43
|
}))
|
|
43
44
|
.views(self => ({
|
|
45
|
+
/**
|
|
46
|
+
* #getter
|
|
47
|
+
*/
|
|
44
48
|
get root() {
|
|
45
49
|
return (0, mobx_state_tree_1.getParent)(self);
|
|
46
50
|
},
|