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AssemblyManager

Note: this document is automatically generated from mobx-state-tree objects in our source code. See Core concepts and intro to pluggable elements for more info

Source file​

packages/core/assemblyManager/assemblyManager.ts

AssemblyManager - Properties​

property: assemblies​

this is automatically managed by an autorun which looks in the parent session.assemblies, session.sessionAssemblies, and session.temporaryAssemblies

// type signature
IArrayType<IModelType<{ configuration: IMaybe<IReferenceType<IAnyType>>; }, { error: unknown; loaded: boolean; loadingP: Promise<void>; volatileRegions: BasicRegion[]; refNameAliases: RefNameAliases; lowerCaseRefNameAliases: RefNameAliases; cytobands: Feature[]; } & ... 5 more ... & { ...; }, _NotCustomized, _NotCus...
// code
assemblies: types.array(assemblyFactory(conf, pm))

AssemblyManager - Getters​

getter: assemblyNamesList​

// type
any

getter: assemblyList​

looks at jbrowse.assemblies, session.sessionAssemblies, and session.temporaryAssemblies to load from

// type
({ [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode<AnyConfigurationSchemaType>)[]

AssemblyManager - Methods​

method: get​

// type signature
get: (asmName: string) => { configuration: any; } & NonEmptyObject & { error: unknown; loaded: boolean; loadingP: Promise<void>; volatileRegions: BasicRegion[]; refNameAliases: RefNameAliases; lowerCaseRefNameAliases: RefNameAliases; cytobands: Feature[]; } & ... 6 more ... & IStateTreeNode<...>

method: waitForAssembly​

use this method instead of assemblyManager.get(assemblyName) to get an assembly with regions loaded

// type signature
waitForAssembly: (assemblyName: string) => Promise<{ configuration: any; } & NonEmptyObject & { error: unknown; loaded: boolean; loadingP: Promise<void>; volatileRegions: BasicRegion[]; refNameAliases: RefNameAliases; lowerCaseRefNameAliases: RefNameAliases; cytobands: Feature[]; } & ... 6 more ... & IStateTreeNode<...>>

method: getRefNameMapForAdapter​

// type signature
getRefNameMapForAdapter: (adapterConf: AdapterConf, assemblyName: string, opts: { signal?: AbortSignal; sessionId: string; }) => Promise<any>

method: getReverseRefNameMapForAdapter​

// type signature
getReverseRefNameMapForAdapter: (adapterConf: AdapterConf, assemblyName: string, opts: { signal?: AbortSignal; sessionId: string; }) => Promise<any>

method: isValidRefName​

// type signature
isValidRefName: (refName: string, assemblyName: string) => boolean

AssemblyManager - Actions​

action: removeAssembly​

private: you would generally want to add to manipulate jbrowse.assemblies, session.sessionAssemblies, or session.temporaryAssemblies instead of using this directly

// type signature
removeAssembly: (asm: { configuration: any; } & NonEmptyObject & { error: unknown; loaded: boolean; loadingP: Promise<void>; volatileRegions: BasicRegion[]; refNameAliases: RefNameAliases; lowerCaseRefNameAliases: RefNameAliases; cytobands: Feature[]; } & ... 6 more ... & IStateTreeNode<...>) => void

action: addAssembly​

private: you would generally want to add to manipulate jbrowse.assemblies, session.sessionAssemblies, or session.temporaryAssemblies instead of using this directly

this can take an active instance of an assembly, in which case it is referred to, or it can take an identifier e.g. assembly name, which is used as a reference. snapshots cannot be used

// type signature
addAssembly: (configuration: any) => void

action: replaceAssembly​

private: you would generally want to add to manipulate jbrowse.assemblies, session.sessionAssemblies, or session.temporaryAssemblies instead of using this directly

// type signature
replaceAssembly: (idx: number, configuration: any) => void