Assembly
Note: this document is automatically generated from @jbrowse/mobx-state-tree objects in our source code. See Core concepts and intro to pluggable elements for more info
Also note: this document represents the state model API for the current released version of jbrowse. If you are not using the current version, please cross reference the markdown files in our repo of the checked out git tag
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Assembly - Properties
property: configuration
// type signature
IMaybe<IReferenceType<IAnyType>>
// code
configuration: types.safeReference(assemblyConfigType)
Assembly - Getters
getter: lowerCaseRefNameAliases
// type
{ [k: string]: string; }
getter: initialized
this is a getter with a side effect of loading the data. not the best practice, but it helps to lazy load the assembly
// type
boolean
getter: name
// type
string
getter: regions
// type
BasicRegion[]
getter: aliases
// type
string[]
getter: displayName
// type
string
getter: allAliases
// type
any[]
getter: allRefNames
note: lowerCaseRefNameAliases not included here: this allows the list of refnames to be just the "normal casing", but things like getCanonicalRefName can resolve a lower-case name if needed
// type
string[]
getter: lowerCaseRefNames
// type
string[]
getter: allRefNamesWithLowerCase
// type
any[]
getter: rpcManager
// type
RpcManager
getter: refNameColors
// type
string[]
getter: refNames
// type
string[]
Assembly - Methods
method: getConf
// type signature
getConf: (arg: string) => any
method: hasName
// type signature
hasName: (name: string) => any
method: getCanonicalRefName
Returns the canonical refName for a given alias or refName. Note: The canonical name may differ from what's in the FASTA file when refNameAliases with override:true are configured. To get the name that matches the FASTA file, use getSeqAdapterRefName().
// type signature
getCanonicalRefName: (refName: string) => string
method: getCanonicalRefName2
Returns canonical refName, falling back to input if not found. See getCanonicalRefName() for details.
// type signature
getCanonicalRefName2: (refName: string) => any
method: getRefNameColor
// type signature
getRefNameColor: (refName: string) => string
method: isValidRefName
// type signature
isValidRefName: (refName: string) => boolean
method: getSeqAdapterRefName
Given a canonical refName, returns the refName used by the sequence adapter (what's in the FASTA file). Falls back to the input if no mapping exists.
// type signature
getSeqAdapterRefName: (canonicalRefName: string) => string
method: getAdapterMapEntry
// type signature
getAdapterMapEntry: (adapterConf: AdapterConf, options: BaseOptions) => Promise<RefNameMap>
method: getRefNameMapForAdapter
get Map of canonical-name -> adapter-specific-name
// type signature
getRefNameMapForAdapter: (adapterConf: AdapterConf, opts: BaseOptions) => Promise<any>
method: getReverseRefNameMapForAdapter
get Map of adapter-specific-name -> canonical-name
// type signature
getReverseRefNameMapForAdapter: (adapterConf: AdapterConf, opts: BaseOptions) => Promise<any>
Assembly - Actions
action: setLoaded
// type signature
setLoaded: ({ regions, refNameAliases, cytobands, }: { regions: Region[]; refNameAliases: RefNameAliases; cytobands: Feature[]; }) => void
action: setError
// type signature
setError: (e: unknown) => void
action: setRegions
// type signature
setRegions: (regions: Region[]) => void
action: setRefNameAliases
// type signature
setRefNameAliases: (aliases: RefNameAliases) => void
action: setCytobands
// type signature
setCytobands: (cytobands: Feature[]) => void
action: setCanonicalToSeqAdapterRefNames
// type signature
setCanonicalToSeqAdapterRefNames: (map: Record<string, string>) => void
action: setLoadingP
// type signature
setLoadingP: (p?: Promise<void>) => void
action: load
// type signature
load: () => Promise<void>
action: loadPre
// type signature
loadPre: () => Promise<void>