import(methods)
import(BiocGenerics)
import(RSQLite)
import(S4Vectors)
import(BiocVersion)
import(BiocManager)
import(BiocFileCache)

importFrom(tools, R_user_dir)
importFrom(rappdirs, user_cache_dir)
importFrom(stats, setNames)
importFrom(grDevices, rgb)
importFrom(utils, packageVersion, read.csv, read.delim, unzip,
    capture.output, read.table, .DollarNames
)
importFrom(httr,
    GET, content, parse_url, progress, write_disk,
    stop_for_status, status_code, use_proxy, HEAD, headers
)
importFrom(yaml, yaml.load)
importFrom(interactiveDisplayBase, display)

importMethodsFrom(AnnotationDbi, dbconn, dbfile)
importFrom(AnnotationDbi, dbFileConnect)
importFrom(dplyr,"%>%")
importFrom(dplyr,collect)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###

exportClasses(
    Hub,
    AnnotationHub, AnnotationHubResource
)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in AnnotationHub
###

exportMethods(
    names, length, "$", "[", subset, "[[", as.list, c,
    show, fileName, mcols, dbconn, dbfile
)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in AnnotationHub + export corresponding
### methods
###

export(
    cache, "cache<-", query,
    hubUrl, hubCache, hubDate,
    snapshotDate, "snapshotDate<-",
    getHub, listResources, loadResources,
    package, convertHub, removeResources,
    isLocalHub, "isLocalHub<-", getInfoOnIds
)

exportMethods(
    cache, "cache<-", query, removeResources,
    hubUrl, hubCache, hubDate,
    snapshotDate, "snapshotDate<-",
    getHub, isLocalHub, "isLocalHub<-", getInfoOnIds
)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###

export(
    .Hub, AnnotationHub,
    removeCache,
    getAnnotationHubOption, setAnnotationHubOption,
    possibleDates, mcols,
    .httr_proxy, .hub_option_key, .db_close,
    recordStatus, DispatchClassList, refreshHub
)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S3 methods
###

S3method(.DollarNames, Hub)

S3method(as.list, Hub)

### Also export them thru the export() directive so that (a) they can be
### called directly, (b) tab-completion on the name of the generic shows them,
### and (c) methods() doesn't asterisk them.
export(
    .DollarNames.Hub,
    as.list.Hub
)
