@jbrowse/embedded-core 5.0.0-beta.1 → 5.0.0-beta.11

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.
Files changed (12) hide show
  1. package/esm/EmbeddedSessionMixin.d.ts +250 -759
  2. package/esm/EmbeddedSessionMixin.js +19 -12
  3. package/esm/EmbeddedSessionThemeMixin.d.ts +70 -345
  4. package/esm/EmbeddedSessionThemeMixin.js +31 -22
  5. package/esm/createEmbeddedRootModel.d.ts +192 -454
  6. package/esm/createEmbeddedRootModel.js +29 -16
  7. package/esm/ui/EmbeddedViewContainer.js +8 -8
  8. package/package.json +7 -7
  9. package/esm/ui/VersionAboutDialog.d.ts +0 -5
  10. package/esm/ui/VersionAboutDialog.js +0 -13
  11. package/esm/ui/ViewTitle.d.ts +0 -5
  12. package/esm/ui/ViewTitle.js +0 -65
package/esm/createEmbeddedRootModel.d.ts CHANGED
@@ -32,116 +32,125 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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  configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly defaultDriver: {
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- readonly type: "string";
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- readonly description: "the RPC driver to run data fetching on: MainThreadRpcDriver or WebWorkerRpcDriver. Leave empty to use the default for this application";
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- readonly defaultValue: "";
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- readonly advanced: true;
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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  };
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  readonly workerCount: {
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- readonly type: "number";
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- readonly description: "The number of workers to use. If 0 (the default) JBrowse will decide how many workers to use.";
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- readonly defaultValue: 0;
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- readonly advanced: true;
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+ type: "number";
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+ } & {
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+ defaultValue: number;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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  readonly hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly trackNames: {
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- readonly type: "boolean";
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- readonly defaultValue: false;
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+ type: "boolean";
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+ } & {
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+ defaultValue: boolean;
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  };
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  readonly categories: {
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- readonly type: "boolean";
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- readonly defaultValue: false;
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+ type: "boolean";
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+ } & {
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+ defaultValue: boolean;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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  readonly defaultFolderCategories: {
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- readonly type: "stringArray";
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- readonly description: "list of category names to display as folders by default";
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- readonly defaultValue: readonly [];
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly categoryNames: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly topLevelCategories: {
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- readonly type: "boolean";
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- readonly defaultValue: false;
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+ type: "boolean";
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+ } & {
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+ defaultValue: boolean;
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  };
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  readonly subCategories: {
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- readonly type: "boolean";
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- readonly defaultValue: false;
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+ type: "boolean";
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+ } & {
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+ defaultValue: boolean;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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  readonly preferences: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly animationMode: {
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- readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
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- readonly type: "stringEnum";
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- readonly defaultValue: "enabled";
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+ type: "stringEnum";
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+ } & {
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
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+ } & {
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+ defaultValue: string;
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  };
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  readonly scrollZoom: {
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- readonly type: "boolean";
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- readonly defaultValue: false;
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+ type: "boolean";
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+ } & {
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+ defaultValue: boolean;
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  };
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  readonly numberGrouping: {
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- readonly type: "boolean";
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- readonly defaultValue: true;
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+ type: "boolean";
96
+ } & {
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+ defaultValue: boolean;
91
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  };
92
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  readonly useWorkspaces: {
93
- readonly type: "boolean";
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- readonly defaultValue: false;
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+ type: "boolean";
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+ } & {
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+ defaultValue: boolean;
95
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ readonly developerMode: {
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+ type: "boolean";
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+ } & {
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+ defaultValue: boolean;
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+ };
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
97
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  readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
98
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  readonly feature: {
99
- readonly type: "frozen";
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- readonly description: "adds extra fields to the feature details";
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- readonly defaultValue: {};
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- readonly contextVariable: ["feature"];
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+ type: "frozen";
113
+ } & {
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+ defaultValue: unknown;
103
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  };
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  readonly subfeatures: {
105
- readonly type: "frozen";
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- readonly description: "adds extra fields to the subfeatures of a feature";
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- readonly defaultValue: {};
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- readonly contextVariable: ["feature"];
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+ type: "frozen";
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+ } & {
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+ defaultValue: unknown;
109
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  };
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  readonly depth: {
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- readonly type: "maybeNumber";
112
- readonly description: "levels of subfeature the formatDetails.subfeatures callback runs on, default 2";
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+ type: "maybeNumber";
113
123
  };
114
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  readonly maxDepth: {
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- readonly type: "maybeNumber";
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- readonly description: "hide subfeatures nested deeper than this, default no limit";
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+ type: "maybeNumber";
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
119
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  readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly config: {
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- readonly type: "frozen";
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- readonly description: "formats configuration object in about dialog";
123
- readonly defaultValue: {};
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- readonly contextVariable: ["config"];
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+ type: "frozen";
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+ } & {
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+ defaultValue: unknown;
125
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  };
126
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  readonly hideUris: {
127
- readonly type: "boolean";
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- readonly defaultValue: false;
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+ type: "boolean";
136
+ } & {
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+ defaultValue: boolean;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
139
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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  readonly theme: {
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- readonly type: "frozen";
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- readonly defaultValue: {};
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+ type: "frozen";
142
+ } & {
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+ defaultValue: unknown;
134
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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- assembly: import("@jbrowse/mobx-state-tree").IAnyType;
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- tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
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- internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
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- connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
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- aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
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+ tracks: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown>[] | null | undefined, Record<string, unknown>[], Record<string, unknown>[]>;
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+ internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
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+ connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
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+ aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
141
151
  plugins: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
142
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  }, {
143
- readonly assemblies: any[];
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- readonly assemblyName: string;
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+ readonly assemblyNames: string[];
145
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  readonly rpcManager: RpcManager;
146
155
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
147
156
  /**
@@ -158,7 +167,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
158
167
  error: unknown;
159
168
  loadingP: Promise<void> | undefined;
160
169
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
161
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
170
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
162
171
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
163
172
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
164
173
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -196,7 +205,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
196
205
  afterAttach(): void;
197
206
  } & {
198
207
  readonly initialized: boolean;
199
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
200
208
  readonly allRefNames: string[] | undefined;
201
209
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
202
210
  readonly rpcManager: RpcManager;
@@ -214,6 +222,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
214
222
  getCanonicalRefName2(refName: string): string;
215
223
  isValidRefName(refName: string): boolean;
216
224
  } & {
225
+ getRefNamePosition(refName: string): number | undefined;
217
226
  getAliasesForRefName(refName: string): string[];
218
227
  getRefNameMapForAdapter(adapterConf: {
219
228
  [x: string]: unknown;
@@ -229,141 +238,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
229
238
  } | undefined;
230
239
  };
231
240
  } & {
232
- readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
233
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
234
- }> & {
235
- error: unknown;
236
- loadingP: Promise<void> | undefined;
237
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
238
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
239
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
240
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
241
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
242
- loadedGeneticCodes: Record<string, number> | undefined;
243
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
244
- statusMessage: string | undefined;
245
- statusProgress: number | undefined;
246
- statusSource: string | undefined;
247
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
248
- } & {
249
- getConf(arg: string): any;
250
- } & {
251
- readonly name: string;
252
- readonly aliases: string[];
253
- readonly displayName: string;
254
- readonly refNameColors: string[];
255
- } & {
256
- readonly allAliases: string[];
257
- hasName(name: string): boolean;
258
- } & {
259
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
260
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
261
- } & {
262
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
263
- regions: import("@jbrowse/core/util").Region[];
264
- cytobands: import("@jbrowse/core/util").Feature[];
265
- geneticCodes: Record<string, number>;
266
- }): void;
267
- setError(e: unknown): void;
268
- setLoadingP(p?: Promise<void>): void;
269
- loadPre(): Promise<void>;
270
- } & {
271
- load(): Promise<void>;
272
- } & {
273
- afterAttach(): void;
274
- } & {
275
- readonly initialized: boolean;
276
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
277
- readonly allRefNames: string[] | undefined;
278
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
279
- readonly rpcManager: RpcManager;
280
- } & {
281
- readonly refNames: string[] | undefined;
282
- } & {
283
- readonly refNameToIndex: Map<string, number> | undefined;
284
- } & {
285
- getCanonicalRefName(refName: string): string | undefined;
286
- getRefNameColor(refName: string): string | undefined;
287
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
288
- getGeneticCodeId(refName: string): number;
289
- getSeqAdapterRefName(canonicalRefName: string): string;
290
- } & {
291
- getCanonicalRefName2(refName: string): string;
292
- isValidRefName(refName: string): boolean;
293
- } & {
294
- getAliasesForRefName(refName: string): string[];
295
- getRefNameMapForAdapter(adapterConf: {
296
- [x: string]: unknown;
297
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
298
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
299
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
300
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
301
- }, {
302
- error: unknown;
303
- loadingP: Promise<void> | undefined;
304
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
305
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
306
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
307
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
308
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
309
- loadedGeneticCodes: Record<string, number> | undefined;
310
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
311
- statusMessage: string | undefined;
312
- statusProgress: number | undefined;
313
- statusSource: string | undefined;
314
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
315
- } & {
316
- getConf(arg: string): any;
317
- } & {
318
- readonly name: string;
319
- readonly aliases: string[];
320
- readonly displayName: string;
321
- readonly refNameColors: string[];
322
- } & {
323
- readonly allAliases: string[];
324
- hasName(name: string): boolean;
325
- } & {
326
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
327
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
328
- } & {
329
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
330
- regions: import("@jbrowse/core/util").Region[];
331
- cytobands: import("@jbrowse/core/util").Feature[];
332
- geneticCodes: Record<string, number>;
333
- }): void;
334
- setError(e: unknown): void;
335
- setLoadingP(p?: Promise<void>): void;
336
- loadPre(): Promise<void>;
337
- } & {
338
- load(): Promise<void>;
339
- } & {
340
- afterAttach(): void;
341
- } & {
342
- readonly initialized: boolean;
343
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
344
- readonly allRefNames: string[] | undefined;
345
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
346
- readonly rpcManager: RpcManager;
347
- } & {
348
- readonly refNames: string[] | undefined;
349
- } & {
350
- readonly refNameToIndex: Map<string, number> | undefined;
351
- } & {
352
- getCanonicalRefName(refName: string): string | undefined;
353
- getRefNameColor(refName: string): string | undefined;
354
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
355
- getGeneticCodeId(refName: string): number;
356
- getSeqAdapterRefName(canonicalRefName: string): string;
357
- } & {
358
- getCanonicalRefName2(refName: string): string;
359
- isValidRefName(refName: string): boolean;
360
- } & {
361
- getAliasesForRefName(refName: string): string[];
362
- getRefNameMapForAdapter(adapterConf: {
363
- [x: string]: unknown;
364
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
365
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
366
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
241
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
367
242
  } & {
368
243
  getCanonicalAssemblyName(asmName: string): string | undefined;
369
244
  getDisplayName(asmName: string): string;
@@ -373,7 +248,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
373
248
  error: unknown;
374
249
  loadingP: Promise<void> | undefined;
375
250
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
376
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
251
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
377
252
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
378
253
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
379
254
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -411,7 +286,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
411
286
  afterAttach(): void;
412
287
  } & {
413
288
  readonly initialized: boolean;
414
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
415
289
  readonly allRefNames: string[] | undefined;
416
290
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
417
291
  readonly rpcManager: RpcManager;
@@ -429,6 +303,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
429
303
  getCanonicalRefName2(refName: string): string;
430
304
  isValidRefName(refName: string): boolean;
431
305
  } & {
306
+ getRefNamePosition(refName: string): number | undefined;
432
307
  getAliasesForRefName(refName: string): string[];
433
308
  getRefNameMapForAdapter(adapterConf: {
434
309
  [x: string]: unknown;
@@ -440,7 +315,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
440
315
  error: unknown;
441
316
  loadingP: Promise<void> | undefined;
442
317
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
443
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
318
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
444
319
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
445
320
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
446
321
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -478,7 +353,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
478
353
  afterAttach(): void;
479
354
  } & {
480
355
  readonly initialized: boolean;
481
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
482
356
  readonly allRefNames: string[] | undefined;
483
357
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
484
358
  readonly rpcManager: RpcManager;
@@ -496,6 +370,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
496
370
  getCanonicalRefName2(refName: string): string;
497
371
  isValidRefName(refName: string): boolean;
498
372
  } & {
373
+ getRefNamePosition(refName: string): number | undefined;
499
374
  getAliasesForRefName(refName: string): string[];
500
375
  getRefNameMapForAdapter(adapterConf: {
501
376
  [x: string]: unknown;
@@ -509,7 +384,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
509
384
  error: unknown;
510
385
  loadingP: Promise<void> | undefined;
511
386
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
512
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
387
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
513
388
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
514
389
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
515
390
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -547,7 +422,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
547
422
  afterAttach(): void;
548
423
  } & {
549
424
  readonly initialized: boolean;
550
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
551
425
  readonly allRefNames: string[] | undefined;
552
426
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
553
427
  readonly rpcManager: RpcManager;
@@ -565,6 +439,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
565
439
  getCanonicalRefName2(refName: string): string;
566
440
  isValidRefName(refName: string): boolean;
567
441
  } & {
442
+ getRefNamePosition(refName: string): number | undefined;
568
443
  getAliasesForRefName(refName: string): string[];
569
444
  getRefNameMapForAdapter(adapterConf: {
570
445
  [x: string]: unknown;
@@ -576,7 +451,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
576
451
  error: unknown;
577
452
  loadingP: Promise<void> | undefined;
578
453
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
579
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
454
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
580
455
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
581
456
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
582
457
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -614,7 +489,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
614
489
  afterAttach(): void;
615
490
  } & {
616
491
  readonly initialized: boolean;
617
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
618
492
  readonly allRefNames: string[] | undefined;
619
493
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
620
494
  readonly rpcManager: RpcManager;
@@ -632,6 +506,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
632
506
  getCanonicalRefName2(refName: string): string;
633
507
  isValidRefName(refName: string): boolean;
634
508
  } & {
509
+ getRefNamePosition(refName: string): number | undefined;
635
510
  getAliasesForRefName(refName: string): string[];
636
511
  getRefNameMapForAdapter(adapterConf: {
637
512
  [x: string]: unknown;
@@ -639,11 +514,8 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
639
514
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
640
515
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
641
516
  readonly assemblyNamesList: string[];
642
- readonly configuredAssemblyNames: Set<string>;
643
- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
644
- setSubschema(slotName: string, data: Record<string, unknown>): any;
645
- setSlot(slotName: string, value: unknown): void;
646
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
517
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
518
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
647
519
  readonly rpcManager: RpcManager;
648
520
  } & {
649
521
  settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -654,7 +526,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
654
526
  error: unknown;
655
527
  loadingP: Promise<void> | undefined;
656
528
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
657
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
529
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
658
530
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
659
531
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
660
532
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -692,7 +564,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
692
564
  afterAttach(): void;
693
565
  } & {
694
566
  readonly initialized: boolean;
695
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
696
567
  readonly allRefNames: string[] | undefined;
697
568
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
698
569
  readonly rpcManager: RpcManager;
@@ -710,6 +581,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
710
581
  getCanonicalRefName2(refName: string): string;
711
582
  isValidRefName(refName: string): boolean;
712
583
  } & {
584
+ getRefNamePosition(refName: string): number | undefined;
713
585
  getAliasesForRefName(refName: string): string[];
714
586
  getRefNameMapForAdapter(adapterConf: {
715
587
  [x: string]: unknown;
@@ -721,7 +593,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
721
593
  error: unknown;
722
594
  loadingP: Promise<void> | undefined;
723
595
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
724
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
596
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
725
597
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
726
598
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
727
599
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -759,7 +631,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
759
631
  afterAttach(): void;
760
632
  } & {
761
633
  readonly initialized: boolean;
762
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
763
634
  readonly allRefNames: string[] | undefined;
764
635
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
765
636
  readonly rpcManager: RpcManager;
@@ -777,6 +648,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
777
648
  getCanonicalRefName2(refName: string): string;
778
649
  isValidRefName(refName: string): boolean;
779
650
  } & {
651
+ getRefNamePosition(refName: string): number | undefined;
780
652
  getAliasesForRefName(refName: string): string[];
781
653
  getRefNameMapForAdapter(adapterConf: {
782
654
  [x: string]: unknown;
@@ -789,7 +661,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
789
661
  error: unknown;
790
662
  loadingP: Promise<void> | undefined;
791
663
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
792
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
664
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
793
665
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
794
666
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
795
667
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -827,7 +699,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
827
699
  afterAttach(): void;
828
700
  } & {
829
701
  readonly initialized: boolean;
830
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
831
702
  readonly allRefNames: string[] | undefined;
832
703
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
833
704
  readonly rpcManager: RpcManager;
@@ -845,6 +716,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
845
716
  getCanonicalRefName2(refName: string): string;
846
717
  isValidRefName(refName: string): boolean;
847
718
  } & {
719
+ getRefNamePosition(refName: string): number | undefined;
848
720
  getAliasesForRefName(refName: string): string[];
849
721
  getRefNameMapForAdapter(adapterConf: {
850
722
  [x: string]: unknown;
@@ -856,7 +728,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
856
728
  error: unknown;
857
729
  loadingP: Promise<void> | undefined;
858
730
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
859
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
731
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
860
732
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
861
733
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
862
734
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -894,7 +766,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
894
766
  afterAttach(): void;
895
767
  } & {
896
768
  readonly initialized: boolean;
897
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
898
769
  readonly allRefNames: string[] | undefined;
899
770
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
900
771
  readonly rpcManager: RpcManager;
@@ -912,6 +783,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
912
783
  getCanonicalRefName2(refName: string): string;
913
784
  isValidRefName(refName: string): boolean;
914
785
  } & {
786
+ getRefNamePosition(refName: string): number | undefined;
915
787
  getAliasesForRefName(refName: string): string[];
916
788
  getRefNameMapForAdapter(adapterConf: {
917
789
  [x: string]: unknown;
@@ -930,10 +802,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
930
802
  }>, "internetAccounts"> & {
931
803
  internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
932
804
  }, {
933
- /**
934
- * #volatile
935
- */
936
- error: unknown;
937
805
  /**
938
806
  * #volatile
939
807
  */
@@ -953,6 +821,8 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
953
821
  } & {
954
822
  /**
955
823
  * #action
824
+ * Synchronous: an async caller must
825
+ * `await pluginManager.preloadSessionTypes(snapshot)` first.
956
826
  */
957
827
  setSession(sessionSnapshot: SnapshotIn<SESSION>): void;
958
828
  /**
@@ -973,10 +843,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
973
843
  * #action
974
844
  */
975
845
  renameCurrentSession(sessionName: string): void;
976
- /**
977
- * #action
978
- */
979
- setError(error: unknown): void;
980
846
  } & {
981
847
  /**
982
848
  * #getter
@@ -989,116 +855,125 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
989
855
  configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
990
856
  readonly rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
991
857
  readonly defaultDriver: {
992
- readonly type: "string";
993
- readonly description: "the RPC driver to run data fetching on: MainThreadRpcDriver or WebWorkerRpcDriver. Leave empty to use the default for this application";
994
- readonly defaultValue: "";
995
- readonly advanced: true;
858
+ type: "string";
859
+ } & {
860
+ defaultValue: string;
996
861
  };
997
862
  readonly workerCount: {
998
- readonly type: "number";
999
- readonly description: "The number of workers to use. If 0 (the default) JBrowse will decide how many workers to use.";
1000
- readonly defaultValue: 0;
1001
- readonly advanced: true;
863
+ type: "number";
864
+ } & {
865
+ defaultValue: number;
1002
866
  };
1003
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
867
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
1004
868
  readonly hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1005
869
  readonly sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1006
870
  readonly trackNames: {
1007
- readonly type: "boolean";
1008
- readonly defaultValue: false;
871
+ type: "boolean";
872
+ } & {
873
+ defaultValue: boolean;
1009
874
  };
1010
875
  readonly categories: {
1011
- readonly type: "boolean";
1012
- readonly defaultValue: false;
876
+ type: "boolean";
877
+ } & {
878
+ defaultValue: boolean;
1013
879
  };
1014
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
880
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
1015
881
  readonly defaultFolderCategories: {
1016
- readonly type: "stringArray";
1017
- readonly description: "list of category names to display as folders by default";
1018
- readonly defaultValue: readonly [];
882
+ type: "stringArray";
883
+ } & {
884
+ defaultValue: unknown;
1019
885
  };
1020
886
  readonly defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1021
887
  readonly categoryNames: {
1022
- readonly type: "stringArray";
1023
- readonly defaultValue: readonly [];
888
+ type: "stringArray";
889
+ } & {
890
+ defaultValue: unknown;
1024
891
  };
1025
892
  readonly topLevelCategories: {
1026
- readonly type: "boolean";
1027
- readonly defaultValue: false;
893
+ type: "boolean";
894
+ } & {
895
+ defaultValue: boolean;
1028
896
  };
1029
897
  readonly subCategories: {
1030
- readonly type: "boolean";
1031
- readonly defaultValue: false;
898
+ type: "boolean";
899
+ } & {
900
+ defaultValue: boolean;
1032
901
  };
1033
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
1034
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
902
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
903
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
1035
904
  readonly preferences: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1036
905
  readonly animationMode: {
1037
- readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
1038
- readonly type: "stringEnum";
1039
- readonly defaultValue: "enabled";
906
+ type: "stringEnum";
907
+ } & {
908
+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
909
+ } & {
910
+ defaultValue: string;
1040
911
  };
1041
912
  readonly scrollZoom: {
1042
- readonly type: "boolean";
1043
- readonly defaultValue: false;
913
+ type: "boolean";
914
+ } & {
915
+ defaultValue: boolean;
1044
916
  };
1045
917
  readonly numberGrouping: {
1046
- readonly type: "boolean";
1047
- readonly defaultValue: true;
918
+ type: "boolean";
919
+ } & {
920
+ defaultValue: boolean;
1048
921
  };
1049
922
  readonly useWorkspaces: {
1050
- readonly type: "boolean";
1051
- readonly defaultValue: false;
923
+ type: "boolean";
924
+ } & {
925
+ defaultValue: boolean;
1052
926
  };
1053
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
927
+ readonly developerMode: {
928
+ type: "boolean";
929
+ } & {
930
+ defaultValue: boolean;
931
+ };
932
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
1054
933
  readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1055
934
  readonly feature: {
1056
- readonly type: "frozen";
1057
- readonly description: "adds extra fields to the feature details";
1058
- readonly defaultValue: {};
1059
- readonly contextVariable: ["feature"];
935
+ type: "frozen";
936
+ } & {
937
+ defaultValue: unknown;
1060
938
  };
1061
939
  readonly subfeatures: {
1062
- readonly type: "frozen";
1063
- readonly description: "adds extra fields to the subfeatures of a feature";
1064
- readonly defaultValue: {};
1065
- readonly contextVariable: ["feature"];
940
+ type: "frozen";
941
+ } & {
942
+ defaultValue: unknown;
1066
943
  };
1067
944
  readonly depth: {
1068
- readonly type: "maybeNumber";
1069
- readonly description: "levels of subfeature the formatDetails.subfeatures callback runs on, default 2";
945
+ type: "maybeNumber";
1070
946
  };
1071
947
  readonly maxDepth: {
1072
- readonly type: "maybeNumber";
1073
- readonly description: "hide subfeatures nested deeper than this, default no limit";
948
+ type: "maybeNumber";
1074
949
  };
1075
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
950
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
1076
951
  readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1077
952
  readonly config: {
1078
- readonly type: "frozen";
1079
- readonly description: "formats configuration object in about dialog";
1080
- readonly defaultValue: {};
1081
- readonly contextVariable: ["config"];
953
+ type: "frozen";
954
+ } & {
955
+ defaultValue: unknown;
1082
956
  };
1083
957
  readonly hideUris: {
1084
- readonly type: "boolean";
1085
- readonly defaultValue: false;
958
+ type: "boolean";
959
+ } & {
960
+ defaultValue: boolean;
1086
961
  };
1087
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
962
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
1088
963
  readonly theme: {
1089
- readonly type: "frozen";
1090
- readonly defaultValue: {};
964
+ type: "frozen";
965
+ } & {
966
+ defaultValue: unknown;
1091
967
  };
1092
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
1093
- assembly: import("@jbrowse/mobx-state-tree").IAnyType;
1094
- tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
1095
- internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
1096
- connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
1097
- aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
968
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
969
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
970
+ tracks: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown>[] | null | undefined, Record<string, unknown>[], Record<string, unknown>[]>;
971
+ internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
972
+ connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
973
+ aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
1098
974
  plugins: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1099
975
  }, {
1100
- readonly assemblies: any[];
1101
- readonly assemblyName: string;
976
+ readonly assemblyNames: string[];
1102
977
  readonly rpcManager: RpcManager;
1103
978
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
1104
979
  /**
@@ -1115,7 +990,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1115
990
  error: unknown;
1116
991
  loadingP: Promise<void> | undefined;
1117
992
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1118
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
993
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1119
994
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1120
995
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1121
996
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1153,7 +1028,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1153
1028
  afterAttach(): void;
1154
1029
  } & {
1155
1030
  readonly initialized: boolean;
1156
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1157
1031
  readonly allRefNames: string[] | undefined;
1158
1032
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1159
1033
  readonly rpcManager: RpcManager;
@@ -1171,6 +1045,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1171
1045
  getCanonicalRefName2(refName: string): string;
1172
1046
  isValidRefName(refName: string): boolean;
1173
1047
  } & {
1048
+ getRefNamePosition(refName: string): number | undefined;
1174
1049
  getAliasesForRefName(refName: string): string[];
1175
1050
  getRefNameMapForAdapter(adapterConf: {
1176
1051
  [x: string]: unknown;
@@ -1186,141 +1061,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1186
1061
  } | undefined;
1187
1062
  };
1188
1063
  } & {
1189
- readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1190
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1191
- }> & {
1192
- error: unknown;
1193
- loadingP: Promise<void> | undefined;
1194
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1195
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1196
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1197
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1198
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1199
- loadedGeneticCodes: Record<string, number> | undefined;
1200
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1201
- statusMessage: string | undefined;
1202
- statusProgress: number | undefined;
1203
- statusSource: string | undefined;
1204
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1205
- } & {
1206
- getConf(arg: string): any;
1207
- } & {
1208
- readonly name: string;
1209
- readonly aliases: string[];
1210
- readonly displayName: string;
1211
- readonly refNameColors: string[];
1212
- } & {
1213
- readonly allAliases: string[];
1214
- hasName(name: string): boolean;
1215
- } & {
1216
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1217
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1218
- } & {
1219
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1220
- regions: import("@jbrowse/core/util").Region[];
1221
- cytobands: import("@jbrowse/core/util").Feature[];
1222
- geneticCodes: Record<string, number>;
1223
- }): void;
1224
- setError(e: unknown): void;
1225
- setLoadingP(p?: Promise<void>): void;
1226
- loadPre(): Promise<void>;
1227
- } & {
1228
- load(): Promise<void>;
1229
- } & {
1230
- afterAttach(): void;
1231
- } & {
1232
- readonly initialized: boolean;
1233
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1234
- readonly allRefNames: string[] | undefined;
1235
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1236
- readonly rpcManager: RpcManager;
1237
- } & {
1238
- readonly refNames: string[] | undefined;
1239
- } & {
1240
- readonly refNameToIndex: Map<string, number> | undefined;
1241
- } & {
1242
- getCanonicalRefName(refName: string): string | undefined;
1243
- getRefNameColor(refName: string): string | undefined;
1244
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1245
- getGeneticCodeId(refName: string): number;
1246
- getSeqAdapterRefName(canonicalRefName: string): string;
1247
- } & {
1248
- getCanonicalRefName2(refName: string): string;
1249
- isValidRefName(refName: string): boolean;
1250
- } & {
1251
- getAliasesForRefName(refName: string): string[];
1252
- getRefNameMapForAdapter(adapterConf: {
1253
- [x: string]: unknown;
1254
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1255
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1256
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1257
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1258
- }, {
1259
- error: unknown;
1260
- loadingP: Promise<void> | undefined;
1261
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1262
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1263
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1264
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1265
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1266
- loadedGeneticCodes: Record<string, number> | undefined;
1267
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1268
- statusMessage: string | undefined;
1269
- statusProgress: number | undefined;
1270
- statusSource: string | undefined;
1271
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1272
- } & {
1273
- getConf(arg: string): any;
1274
- } & {
1275
- readonly name: string;
1276
- readonly aliases: string[];
1277
- readonly displayName: string;
1278
- readonly refNameColors: string[];
1279
- } & {
1280
- readonly allAliases: string[];
1281
- hasName(name: string): boolean;
1282
- } & {
1283
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1284
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1285
- } & {
1286
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1287
- regions: import("@jbrowse/core/util").Region[];
1288
- cytobands: import("@jbrowse/core/util").Feature[];
1289
- geneticCodes: Record<string, number>;
1290
- }): void;
1291
- setError(e: unknown): void;
1292
- setLoadingP(p?: Promise<void>): void;
1293
- loadPre(): Promise<void>;
1294
- } & {
1295
- load(): Promise<void>;
1296
- } & {
1297
- afterAttach(): void;
1298
- } & {
1299
- readonly initialized: boolean;
1300
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1301
- readonly allRefNames: string[] | undefined;
1302
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1303
- readonly rpcManager: RpcManager;
1304
- } & {
1305
- readonly refNames: string[] | undefined;
1306
- } & {
1307
- readonly refNameToIndex: Map<string, number> | undefined;
1308
- } & {
1309
- getCanonicalRefName(refName: string): string | undefined;
1310
- getRefNameColor(refName: string): string | undefined;
1311
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1312
- getGeneticCodeId(refName: string): number;
1313
- getSeqAdapterRefName(canonicalRefName: string): string;
1314
- } & {
1315
- getCanonicalRefName2(refName: string): string;
1316
- isValidRefName(refName: string): boolean;
1317
- } & {
1318
- getAliasesForRefName(refName: string): string[];
1319
- getRefNameMapForAdapter(adapterConf: {
1320
- [x: string]: unknown;
1321
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1322
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1323
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1064
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
1324
1065
  } & {
1325
1066
  getCanonicalAssemblyName(asmName: string): string | undefined;
1326
1067
  getDisplayName(asmName: string): string;
@@ -1330,7 +1071,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1330
1071
  error: unknown;
1331
1072
  loadingP: Promise<void> | undefined;
1332
1073
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1333
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1074
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1334
1075
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1335
1076
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1336
1077
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1368,7 +1109,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1368
1109
  afterAttach(): void;
1369
1110
  } & {
1370
1111
  readonly initialized: boolean;
1371
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1372
1112
  readonly allRefNames: string[] | undefined;
1373
1113
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1374
1114
  readonly rpcManager: RpcManager;
@@ -1386,6 +1126,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1386
1126
  getCanonicalRefName2(refName: string): string;
1387
1127
  isValidRefName(refName: string): boolean;
1388
1128
  } & {
1129
+ getRefNamePosition(refName: string): number | undefined;
1389
1130
  getAliasesForRefName(refName: string): string[];
1390
1131
  getRefNameMapForAdapter(adapterConf: {
1391
1132
  [x: string]: unknown;
@@ -1397,7 +1138,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1397
1138
  error: unknown;
1398
1139
  loadingP: Promise<void> | undefined;
1399
1140
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1400
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1141
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1401
1142
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1402
1143
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1403
1144
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1435,7 +1176,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1435
1176
  afterAttach(): void;
1436
1177
  } & {
1437
1178
  readonly initialized: boolean;
1438
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1439
1179
  readonly allRefNames: string[] | undefined;
1440
1180
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1441
1181
  readonly rpcManager: RpcManager;
@@ -1453,6 +1193,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1453
1193
  getCanonicalRefName2(refName: string): string;
1454
1194
  isValidRefName(refName: string): boolean;
1455
1195
  } & {
1196
+ getRefNamePosition(refName: string): number | undefined;
1456
1197
  getAliasesForRefName(refName: string): string[];
1457
1198
  getRefNameMapForAdapter(adapterConf: {
1458
1199
  [x: string]: unknown;
@@ -1466,7 +1207,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1466
1207
  error: unknown;
1467
1208
  loadingP: Promise<void> | undefined;
1468
1209
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1469
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1210
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1470
1211
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1471
1212
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1472
1213
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1504,7 +1245,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1504
1245
  afterAttach(): void;
1505
1246
  } & {
1506
1247
  readonly initialized: boolean;
1507
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1508
1248
  readonly allRefNames: string[] | undefined;
1509
1249
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1510
1250
  readonly rpcManager: RpcManager;
@@ -1522,6 +1262,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1522
1262
  getCanonicalRefName2(refName: string): string;
1523
1263
  isValidRefName(refName: string): boolean;
1524
1264
  } & {
1265
+ getRefNamePosition(refName: string): number | undefined;
1525
1266
  getAliasesForRefName(refName: string): string[];
1526
1267
  getRefNameMapForAdapter(adapterConf: {
1527
1268
  [x: string]: unknown;
@@ -1533,7 +1274,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1533
1274
  error: unknown;
1534
1275
  loadingP: Promise<void> | undefined;
1535
1276
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1536
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1277
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1537
1278
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1538
1279
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1539
1280
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1571,7 +1312,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1571
1312
  afterAttach(): void;
1572
1313
  } & {
1573
1314
  readonly initialized: boolean;
1574
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1575
1315
  readonly allRefNames: string[] | undefined;
1576
1316
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1577
1317
  readonly rpcManager: RpcManager;
@@ -1589,6 +1329,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1589
1329
  getCanonicalRefName2(refName: string): string;
1590
1330
  isValidRefName(refName: string): boolean;
1591
1331
  } & {
1332
+ getRefNamePosition(refName: string): number | undefined;
1592
1333
  getAliasesForRefName(refName: string): string[];
1593
1334
  getRefNameMapForAdapter(adapterConf: {
1594
1335
  [x: string]: unknown;
@@ -1596,11 +1337,8 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1596
1337
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1597
1338
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1598
1339
  readonly assemblyNamesList: string[];
1599
- readonly configuredAssemblyNames: Set<string>;
1600
- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
1601
- setSubschema(slotName: string, data: Record<string, unknown>): any;
1602
- setSlot(slotName: string, value: unknown): void;
1603
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
1340
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
1341
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1604
1342
  readonly rpcManager: RpcManager;
1605
1343
  } & {
1606
1344
  settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1611,7 +1349,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1611
1349
  error: unknown;
1612
1350
  loadingP: Promise<void> | undefined;
1613
1351
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1614
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1352
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1615
1353
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1616
1354
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1617
1355
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1649,7 +1387,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1649
1387
  afterAttach(): void;
1650
1388
  } & {
1651
1389
  readonly initialized: boolean;
1652
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1653
1390
  readonly allRefNames: string[] | undefined;
1654
1391
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1655
1392
  readonly rpcManager: RpcManager;
@@ -1667,6 +1404,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1667
1404
  getCanonicalRefName2(refName: string): string;
1668
1405
  isValidRefName(refName: string): boolean;
1669
1406
  } & {
1407
+ getRefNamePosition(refName: string): number | undefined;
1670
1408
  getAliasesForRefName(refName: string): string[];
1671
1409
  getRefNameMapForAdapter(adapterConf: {
1672
1410
  [x: string]: unknown;
@@ -1678,7 +1416,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1678
1416
  error: unknown;
1679
1417
  loadingP: Promise<void> | undefined;
1680
1418
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1681
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1419
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1682
1420
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1683
1421
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1684
1422
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1716,7 +1454,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1716
1454
  afterAttach(): void;
1717
1455
  } & {
1718
1456
  readonly initialized: boolean;
1719
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1720
1457
  readonly allRefNames: string[] | undefined;
1721
1458
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1722
1459
  readonly rpcManager: RpcManager;
@@ -1734,6 +1471,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1734
1471
  getCanonicalRefName2(refName: string): string;
1735
1472
  isValidRefName(refName: string): boolean;
1736
1473
  } & {
1474
+ getRefNamePosition(refName: string): number | undefined;
1737
1475
  getAliasesForRefName(refName: string): string[];
1738
1476
  getRefNameMapForAdapter(adapterConf: {
1739
1477
  [x: string]: unknown;
@@ -1746,7 +1484,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1746
1484
  error: unknown;
1747
1485
  loadingP: Promise<void> | undefined;
1748
1486
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1749
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1487
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1750
1488
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1751
1489
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1752
1490
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1784,7 +1522,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1784
1522
  afterAttach(): void;
1785
1523
  } & {
1786
1524
  readonly initialized: boolean;
1787
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1788
1525
  readonly allRefNames: string[] | undefined;
1789
1526
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1790
1527
  readonly rpcManager: RpcManager;
@@ -1802,6 +1539,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1802
1539
  getCanonicalRefName2(refName: string): string;
1803
1540
  isValidRefName(refName: string): boolean;
1804
1541
  } & {
1542
+ getRefNamePosition(refName: string): number | undefined;
1805
1543
  getAliasesForRefName(refName: string): string[];
1806
1544
  getRefNameMapForAdapter(adapterConf: {
1807
1545
  [x: string]: unknown;
@@ -1813,7 +1551,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1813
1551
  error: unknown;
1814
1552
  loadingP: Promise<void> | undefined;
1815
1553
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1816
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1554
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1817
1555
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1818
1556
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1819
1557
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1851,7 +1589,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1851
1589
  afterAttach(): void;
1852
1590
  } & {
1853
1591
  readonly initialized: boolean;
1854
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1855
1592
  readonly allRefNames: string[] | undefined;
1856
1593
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1857
1594
  readonly rpcManager: RpcManager;
@@ -1869,6 +1606,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1869
1606
  getCanonicalRefName2(refName: string): string;
1870
1607
  isValidRefName(refName: string): boolean;
1871
1608
  } & {
1609
+ getRefNamePosition(refName: string): number | undefined;
1872
1610
  getAliasesForRefName(refName: string): string[];
1873
1611
  getRefNameMapForAdapter(adapterConf: {
1874
1612
  [x: string]: unknown;