@jbrowse/product-core 2.8.0 → 2.10.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/RootModel/BaseRootModel.d.ts +102 -56
- package/dist/RootModel/FormatDetails.d.ts +10 -1
- package/dist/RootModel/FormatDetails.js +11 -2
- 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 +290 -117
- package/dist/Session/Tracks.d.ts +309 -98
- package/esm/RootModel/BaseRootModel.d.ts +102 -56
- package/esm/RootModel/FormatDetails.d.ts +10 -1
- package/esm/RootModel/FormatDetails.js +11 -2
- 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 +290 -117
- package/esm/Session/Tracks.d.ts +309 -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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@@ -199,11 +213,17 @@ 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")._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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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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} & {
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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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}, 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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}, assemblyName: string | undefined, opts: {
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}): Promise<{
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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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loadingP: Promise<void> | 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 allRefNamesWithLowerCase: string[] | undefined;
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readonly rpcManager: RpcManager;
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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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volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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} | undefined;
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*/
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+
} | undefined;
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543
584
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cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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544
585
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} & {
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545
586
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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
|
|
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
602
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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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568
607
|
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 */
|
|
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
611
|
setRefNameAliases(aliases: {
|
|
@@ -578,11 +618,17 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
|
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578
618
|
load(): Promise<void>;
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579
619
|
loadPre(): Promise<void>;
|
|
580
620
|
} & {
|
|
581
|
-
getAdapterMapEntry(adapterConf:
|
|
582
|
-
|
|
621
|
+
getAdapterMapEntry(adapterConf: {
|
|
622
|
+
[x: string]: unknown;
|
|
623
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
|
|
624
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
625
|
+
[x: string]: unknown;
|
|
626
|
+
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
583
627
|
[x: string]: string | undefined;
|
|
584
628
|
}>;
|
|
585
|
-
getReverseRefNameMapForAdapter(adapterConf:
|
|
629
|
+
getReverseRefNameMapForAdapter(adapterConf: {
|
|
630
|
+
[x: string]: unknown;
|
|
631
|
+
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
586
632
|
[x: string]: string | undefined;
|
|
587
633
|
}>;
|
|
588
634
|
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
|
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
/**
|
|
2
2
|
* #config FormatDetails
|
|
3
|
-
* generally exists on the config.json or
|
|
3
|
+
* generally exists on the tracks in the config.json or as a 'session' config as
|
|
4
|
+
* configuration.formatDetails
|
|
4
5
|
*/
|
|
5
6
|
export declare function FormatDetailsConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
6
7
|
/**
|
|
@@ -29,4 +30,12 @@ export declare function FormatDetailsConfigSchemaFactory(): import("@jbrowse/cor
|
|
|
29
30
|
defaultValue: number;
|
|
30
31
|
description: string;
|
|
31
32
|
};
|
|
33
|
+
/**
|
|
34
|
+
* #slot configuration.formatDetails.maxDepth
|
|
35
|
+
*/
|
|
36
|
+
maxDepth: {
|
|
37
|
+
type: string;
|
|
38
|
+
defaultValue: number;
|
|
39
|
+
description: string;
|
|
40
|
+
};
|
|
32
41
|
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
@@ -4,7 +4,8 @@ exports.FormatDetailsConfigSchemaFactory = void 0;
|
|
|
4
4
|
const configuration_1 = require("@jbrowse/core/configuration");
|
|
5
5
|
/**
|
|
6
6
|
* #config FormatDetails
|
|
7
|
-
* generally exists on the config.json or
|
|
7
|
+
* generally exists on the tracks in the config.json or as a 'session' config as
|
|
8
|
+
* configuration.formatDetails
|
|
8
9
|
*/
|
|
9
10
|
function FormatDetailsConfigSchemaFactory() {
|
|
10
11
|
return (0, configuration_1.ConfigurationSchema)('FormatDetails', {
|
|
@@ -32,7 +33,15 @@ function FormatDetailsConfigSchemaFactory() {
|
|
|
32
33
|
depth: {
|
|
33
34
|
type: 'number',
|
|
34
35
|
defaultValue: 2,
|
|
35
|
-
description: 'depth to iterate on subfeatures',
|
|
36
|
+
description: 'depth to iterate the formatDetails->subfeatures callback on subfeatures (used for example to only apply the callback to the first layer of subfeatures)',
|
|
37
|
+
},
|
|
38
|
+
/**
|
|
39
|
+
* #slot configuration.formatDetails.maxDepth
|
|
40
|
+
*/
|
|
41
|
+
maxDepth: {
|
|
42
|
+
type: 'number',
|
|
43
|
+
defaultValue: 10000,
|
|
44
|
+
description: 'hide subfeatures greater than a certain depth',
|
|
36
45
|
},
|
|
37
46
|
});
|
|
38
47
|
}
|
|
@@ -4,7 +4,8 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
|
|
|
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
|
},
|